WorldWideScience

Sample records for acid substitution model

  1. Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes.

    Sanzo Miyazawa

    Full Text Available BACKGROUND: Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG and codon (KHG substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. RESULTS: Akaike information criterion (AIC values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. CONCLUSIONS/SIGNIFICANCE: The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.

  2. A New Hybrid Model of Amino Acid Substitution for Protein Functional Classification

    Ke Long WANG; Zhi Ning WEN; Fu Sheng NIE; Meng Long LI

    2005-01-01

    In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by calculating Fisher weights, which can denote how much the variants contribute to the classification.

  3. An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.

    Wang, Huai-Chun; Susko, Edward; Roger, Andrew J

    2014-04-01

    Standard protein phylogenetic models use fixed rate matrices of amino acid interchange derived from analyses of large databases. Differences between the stationary amino acid frequencies of these rate matrices from those of a data set of interest are typically adjusted for by matrix multiplication that converts the empirical rate matrix to an exchangeability matrix which is then postmultiplied by the amino acid frequencies in the alignment. The result is a time-reversible rate matrix with stationary amino acid frequencies equal to the data set frequencies. On the basis of population genetics principles, we develop an amino acid substitution-selection model that parameterizes the fitness of an amino acid as the logarithm of the ratio of the frequency of the amino acid to the frequency of the same amino acid under no selection. The model gives rise to a different sequence of matrix multiplications to convert an empirical rate matrix to one that has stationary amino acid frequencies equal to the data set frequencies. We incorporated the substitution-selection model with an improved amino acid class frequency mixture (cF) model to partially take into account site-specific amino acid frequencies in the phylogenetic models. We show that 1) the selection models fit data significantly better than corresponding models without selection for most of the 21 test data sets; 2) both cF and cF selection models favored the phylogenetic trees that were inferred under current sophisticated models and methods for three difficult phylogenetic problems (the positions of microsporidia and breviates in eukaryote phylogeny and the position of the root of the angiosperm tree); and 3) for data simulated under site-specific residue frequencies, the cF selection models estimated trees closer to the generating trees than a standard Г model or cF without selection. We also explored several ways of estimating amino acid frequencies under neutral evolution that are required for these selection

  4. Evaluating rare amino acid substitutions (RGC_CAMs in a yeast model clade.

    Kenneth Polzin

    Full Text Available When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC_CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC_CAM substitutions by examining their degree of homoplasy and internode certainty in nearly 2.7 million aligned amino acid sites from 5,261 proteins from five species belonging to the yeast Saccharomyces sensu stricto clade whose phylogeny is well-established. We identified 2,647 sites containing RGC_CAM substitutions, a number that contrasts sharply with the 100,887 sites containing RGC_non-CAM substitutions (i.e., changes between amino acids that require only a single nucleotide substitution. We found that RGC_CAM substitutions had significantly lower homoplasy than RGC_non-CAM ones; specifically RGC_CAM substitutions showed a per-site average homoplasy index of 0.100, whereas RGC_non-CAM substitutions had a homoplasy index of 0.215. Internode certainty values were also higher for sites containing RGC_CAM substitutions than for RGC_non-CAM ones. These results suggest that RGC_CAM substitutions possess a strong phylogenetic signal and are useful markers for phylogenetic inference despite their rarity.

  5. Trends in Substitution Models of Molecular Evolution

    Miguel eArenas

    2015-10-01

    Full Text Available Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost forty years after the development of first substitution models, highly sophisticated and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.

  6. Radiation chemistry of salicylic and methyl substituted salicylic acids: Models for the radiation chemistry of pharmaceutical compounds

    Ayatollahi, Shakiba; Kalnina, Daina; Song, Weihua; Turks, Maris; Cooper, William J.

    2013-11-01

    Salicylic acid and its derivatives are components of many medications and moieties found in numerous pharmaceutical compounds. They have been used as models for various pharmaceutical compounds in pharmacological studies, for the treatment of pharmaceuticals and personal care products (PPCPs), and, reactions with natural organic matter (NOM). In this study, the radiation chemistry of benzoic acid, salicylic acid and four methyl substituted salicylic acids (MSA) is reported. The absolute bimolecular reaction rate constants for hydroxyl radical reaction with benzoic and salicylic acids as well as 3-methyl-, 4-methyl-, 5-methyl-, and 6-methyl-salicylic acid were determined (5.86±0.54)×109, (1.07±0.07)×1010, (7.48±0.17)×109, (7.31±0.29)×109, (5.47±0.25)×109, (6.94±0.10)×109 (M-1 s-1), respectively. The hydrated electron reaction rate constants were measured (3.02±0.10)×109, (8.98±0.27)×109, (5.39±0.21)×109, (4.33±0.17)×109, (4.72±0.15)×109, (1.42±0.02)×109 (M-1 s-1), respectively. The transient absorption spectra for the six model compounds were examined and their role as model compounds for the radiation chemistry of pharmaceuticals investigated.

  7. Substituted Indoleacetic Acids Tested in Tissue Cultures

    Engvild, Kjeld Christensen

    1978-01-01

    Monochloro substituted IAA inhibited shoot induction in tobacco tissue cultures about as much as IAA. Dichloro substituted IAA inhibited shoot formation less. Other substituted IAA except 5-fluoro- and 5-bromoindole-3-acetic acid were less active than IAA. Callus growth was quite variable...

  8. ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.

    Whelan, Simon; Allen, James E; Blackburne, Benjamin P; Talavera, David

    2015-01-01

    Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/.

  9. Capillary Electrophoresis of Substituted Benzoic Acids

    Mills, Nancy S.; Spence, John D.; Bushey, Michelle M.

    2005-01-01

    A series of substituted benzoic acids (SBAs) are prepared by students. The pKa shift, a result of the electron-withdrawing or electron-donating characteristics of the subsistent is examined in reference to the electrophoretic migration behavior of benzoic acid.

  10. Biological activities of substituted trichostatic acid derivatives

    Cédric Charrier; Joëlle Roche; Jean-Pierre Gesson; Philippe Bertrand

    2009-07-01

    New substituted trichostatic acid derivatives have been synthesized and evaluated for their biological activities towards the H661 non-small lung cancer cell line. These syntheses were achieved by alkylation of propiophenones to introduce the side chain with a terminal precursor of hydroxamic acid and aminobenzamide derivatives. The first fluorinated derivatives of trichostatic acid are described, such as 6-fluoro trichostatin A, with antiproliferative activities in the micromolar range and with histone deacetylase inhibitory activity.

  11. Bayesian comparisons of codon substitution models.

    Rodrigue, Nicolas; Lartillot, Nicolas; Philippe, Hervé

    2008-11-01

    In 1994, Muse and Gaut (MG) and Goldman and Yang (GY) proposed evolutionary models that recognize the coding structure of the nucleotide sequences under study, by defining a Markovian substitution process with a state space consisting of the 61 sense codons (assuming the universal genetic code). Several variations and extensions to their models have since been proposed, but no general and flexible framework for contrasting the relative performance of alternative approaches has yet been applied. Here, we compute Bayes factors to evaluate the relative merit of several MG and GY styles of codon substitution models, including recent extensions acknowledging heterogeneous nonsynonymous rates across sites, as well as selective effects inducing uneven amino acid or codon preferences. Our results on three real data sets support a logical model construction following the MG formulation, allowing for a flexible account of global amino acid or codon preferences, while maintaining distinct parameters governing overall nucleotide propensities. Through posterior predictive checks, we highlight the importance of such a parameterization. Altogether, the framework presented here suggests a broad modeling project in the MG style, stressing the importance of combining and contrasting available model formulations and grounding developments in a sound probabilistic paradigm.

  12. Quantitative Structure–Property Relationship (QSPR Models for a Local Quantum Descriptor: Investigation of the 4- and 3-Substituted-Cinnamic Acid Esterification

    Cláudio E. Rodrigues-Santos

    2015-09-01

    Full Text Available In this work, the theoretical description of the 4- and 3-substituted-cinnamic acid esterification with different electron donating and electron withdrawing groups was performed at the B3LYP and M06-2X levels, as a two-step process: the O-protonation and the nucleophile attack by ethanol. In parallel, an experimental work devoted to the synthesis and characterization of the substituted-cinnamate esters has also been performed. In order to quantify the substituents effects, quantitative structure–property relationship (QSPR models based on the atomic charges, Fukui functions and the Frontier Effective-for-Reaction Molecular Orbitals (FERMO energies were investigated. In fact, the Fukui functions, ƒ+C and ƒ−O, indicated poor correlations for each individual step, and in contrast with the general literature, the O-protonation step is affected both by the FERMO energies and the O-charges of the carbonyl group. Since the process was shown to not be totally described by either charge- or frontier-orbitals, it is proposed to be frontier-charge-miscere controlled. Moreover, the observed trend for the experimental reaction yields suggests that the electron withdrawing groups favor the reaction and the same was observed for Step 2, which can thus be pointed out as the determining step.

  13. Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog.

    Fu, Mingchuan; Huang, Zhuoran; Mao, Yuanhui; Tao, Shiheng

    2014-09-10

    Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues.

  14. Neighbor Preferences of Amino Acids and Context-Dependent Effects of Amino Acid Substitutions in Human, Mouse, and Dog

    Mingchuan Fu

    2014-09-01

    Full Text Available Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues.

  15. Synthesis and Bioassay of 4-Substituted 2-Oxoglutaric Acids

    Qiu Yun CHEN; Qing Shan LIU; Christopher J. SCHOFIELD

    2006-01-01

    Three 2-oxoglutaric acid analogues were synthesized. Their interaction with factorinhibiting hypoxia-inducible factor (FIH) was studied using LC-MS method. The results show that hydrophobic substitutes of 2-oxoglutaric acids have great influence on their inhibitor activity.

  16. Amine substitution into sulfuric acid – ammonia clusters

    O. Kupiainen

    2011-11-01

    Full Text Available The substitution of ammonia by dimethylamine in sulfuric acid – ammonia – dimethylamine clusters was studied using a collision and evaporation dynamics model. Quantum chemical formation free energies were computed using B3LYP/CBSB7 for geometries and frequencies and RI-CC2/aug-cc-pV(T+dZ for electronic energies. We first demonstrate the good performance of our method by a comparison with an experimental study investigating base substitution in positively charged clusters, and then continue by simulating base exchange in neutral clusters, which cannot be measured directly. Collisions of a dimethylamine molecule with an ammonia containing positively charged cluster result in the instantaneous evaporation of an ammonia molecule, while the dimethylamine molecule remains in the cluster. According to our simulations, a similar base exchange can take place in neutral clusters, although the overall process is more complicated. Neutral sulfuric acid – ammonia clusters are significantly less stable than their positively charged counterparts, resulting in a competition between cluster evaporation and base exchange.

  17. Amino acid derived 1,4-dialkyl substituted imidazolones

    Diness, Frederik; Meldal, Morten Peter

    2010-01-01

    A general method for synthesis of 1,4-substituted imidazolones from amino acids on solid support or in solution has been developed. Amino acid derived 3-Boc-(1,3)-oxazinane (Box) protected amino aldehyde building blocks were coupled through urea bonds to the amino terminal of dipeptides or amino...

  18. Modeling competitive substitution in a polyelectrolyte complex

    Peng, B.; Muthukumar, M., E-mail: muthu@polysci.umass.edu [Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003 (United States)

    2015-12-28

    We have simulated the invasion of a polyelectrolyte complex made of a polycation chain and a polyanion chain, by another longer polyanion chain, using the coarse-grained united atom model for the chains and the Langevin dynamics methodology. Our simulations reveal many intricate details of the substitution reaction in terms of conformational changes of the chains and competition between the invading chain and the chain being displaced for the common complementary chain. We show that the invading chain is required to be sufficiently longer than the chain being displaced for effecting the substitution. Yet, having the invading chain to be longer than a certain threshold value does not reduce the substitution time much further. While most of the simulations were carried out in salt-free conditions, we show that presence of salt facilitates the substitution reaction and reduces the substitution time. Analysis of our data shows that the dominant driving force for the substitution process involving polyelectrolytes lies in the release of counterions during the substitution.

  19. Genotoxic effect of substituted phenoxyacetic acids.

    Venkov, P; Topashka-Ancheva, M; Georgieva, M; Alexieva, V; Karanov, E

    2000-11-01

    The potential toxic and mutagenic action of 2,4-dichlorophenoxyacetic acid has been studied in different test systems, and the obtained results range from increased chromosomal damage to no effect at all. We reexamined the effect of this herbicide by simultaneous using three tests based on yeast, transformed hematopoietic, and mouse bone marrow cells. The results obtained demonstrated that 2,4-dichlorophenoxyacetic acid has cytotoxic and mutagenic effects. The positive response of yeast and transformed hematopoietic cells was verified in kinetics and dose-response experiments. The analysis of metaphase chromosomes indicated a statistically proved induction of breaks, deletions, and exchanges after the intraperitoneal administration of 2,4-dichlorophenoxyacetic acid in mice. The study of phenoxyacetic acid and its differently chlorinated derivatives showed that cytotoxicity and mutagenicity are induced by chlorine atoms at position 2 and/or 4 in the benzene ring. The mutagenic effect was abolished by introduction of a third chlorine atom at position 5. Thus 2,4,5-trichlorophenoxyacetic acid was found to have very weak, if any mutagenic effect; however, the herbicide preserved its toxic effect.

  20. Aspartic acid substitutions affect proton translocation by bacteriorhodopsin.

    Mogi, T; Stern, L J; Marti, T; Chao, B H; Khorana, H G

    1988-01-01

    We have substituted each of the aspartic acid residues in bacteriorhodopsin to determine their possible role in proton translocation by this protein. The aspartic acid residues were replaced by asparagines; in addition, Asp-85, -96, -115, and -112 were changed to glutamic acid and Asp-212 was also replaced by alanine. The mutant bacteriorhodopsin genes were expressed in Escherichia coli and the proteins were purified. The mutant proteins all regenerated bacteriorhodopsin-like chromophores when treated with a detergent-phospholipid mixture and retinal. However, the rates of regeneration of the chromophores and their lambda max varied widely. No support was obtained for the external point charge model for the opsin shift. The Asp-85----Asn mutant showed not detectable proton pumping, the Asp-96----Asn and Asp-212----Glu mutants showed less than 10% and the Asp-115----Glu mutant showed approximately equal to 30% of the normal proton pumping. The implications of these findings for possible mechanisms of proton translocation by bacteriorhodopsin are discussed. PMID:3288985

  1. Simulating an Optimizing Model of Currency Substitution Simulating an Optimizing Model of Currency Substitution

    Leonardo Leiderman

    1992-03-01

    Full Text Available Simulating an Optimizing Model of Currency Substitution This paper reports simulations based on the parameter estimates of an intertemporal model of currency substitution under nonexpected utility obtained by Bufman and Leiderman (1991. Here we first study the quantitative impact of changes in the degree of dollarization and in the elasticity of currency substitution on government seigniorage. Then, when examine whether the model can account for the comovement of consumption growth and assets' returnr after the 1985 stabilization program, and in particular for the consumption boom of 1986-87. The results are generally encouraging for future applications of optimizing models of currencysubstitution to policy and practical issues.

  2. Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors

    Zimmermann Karel

    2010-01-01

    Full Text Available Abstract Background Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. Results We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. Conclusions This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

  3. Mapping of amino acid substitutions conferring herbicide resistance in wheat glutathione transferase.

    Govindarajan, Sridhar; Mannervik, Bengt; Silverman, Joshua A; Wright, Kathy; Regitsky, Drew; Hegazy, Usama; Purcell, Thomas J; Welch, Mark; Minshull, Jeremy; Gustafsson, Claes

    2015-03-20

    We have used design of experiments (DOE) and systematic variance to efficiently explore glutathione transferase substrate specificities caused by amino acid substitutions. Amino acid substitutions selected using phylogenetic analysis were synthetically combined using a DOE design to create an information-rich set of gene variants, termed infologs. We used machine learning to identify and quantify protein sequence-function relationships against 14 different substrates. The resulting models were quantitative and predictive, serving as a guide for engineering of glutathione transferase activity toward a diverse set of herbicides. Predictive quantitative models like those presented here have broad applicability for bioengineering.

  4. Rate constants for 1,5- and 1,6-hydrogen atom transfer reactions of mono-, di-, and tri-aryl-substituted donors, models for hydrogen atom transfers in polyunsaturated fatty acid radicals.

    DeZutter, Christopher B; Horner, John H; Newcomb, Martin

    2008-03-06

    Rate constants for 1,5- and 1,6-hydrogen atom transfer reactions in models of polyunsaturated fatty acid radicals were measured via laser flash photolysis methods. Photolyses of PTOC (pyridine-2-thioneoxycarbonyl) ester derivatives of carboxylic acids gave primary alkyl radicals that reacted by 1,5-hydrogen transfer from mono-, di-, and tri-aryl-substituted positions or 1,6-hydrogen transfer from di- and tri-aryl-substituted positions to give UV-detectable products. Rate constants for reactions in acetonitrile at room temperature ranged from 1 x 10(4) to 4 x 10(6) s(-1). The activation energies for a matched pair of 1,5- and 1,6-hydrogen atom transfers giving tri-aryl-substituted radicals were approximately equal, as were the primary kinetic isotope effects, but the 1,5-hydrogen atom transfer reaction was 1 order of magnitude faster at room temperature than the 1,6-hydrogen atom transfer reaction due to a less favorable entropy of activation for the 1,6-transfer reaction. Solvent effects on the rate constants for the 1,5-hydrogen atom transfer reaction of the 2-[2-(diphenylmethyl)phenyl]ethyl radical at ambient temperature were as large as a factor of 2 with the reaction increasing in rate in lower polarity solvents. Hybrid density functional theory computations for the 1,5- and 1,6-hydrogen atom transfers of the tri-aryl-substituted donors were in qualitative agreement with the experimental results.

  5. Tracing hybrid incompatibilities to single amino acid substitutions.

    Harrison, J Scott; Burton, Ronald S

    2006-03-01

    Deleterious interactions among genes cause reductions in fitness of interpopulation hybrids (hybrid breakdown). Identifying genes involved in hybrid breakdown has proven difficult, and few studies have addressed the molecular basis of this widespread phenomenon. Because proper function of the mitochondrial electron transport system (ETS) requires a coadapted set of nuclear and mitochondrial gene products, ETS genes present an attractive system for studying the evolution of coadapted gene complexes within isolated populations and the loss of fitness in interpopulation hybrids. Here we show the effects of single amino acid substitutions in cytochrome c (CYC) on its functional interaction with another ETS protein, cytochrome c oxidase (COX) in the intertidal copepod Tigriopus californicus. The individual and pairwise consequences of three naturally occurring amino acid substitutions in CYC are examined by site-directed mutagenesis and found to differentially effect the rates of CYC oxidation by COX variants from different source populations. In one case, we show that interpopulation hybrid breakdown in COX activity can be attributed to a single naturally occurring amino acid substitution in CYC.

  6. Selective amino acid substitutions convert the creatine transporter to a gamma-aminobutyric acid transporter.

    Dodd, Joanna R; Christie, David L

    2007-05-25

    The creatine transporter (CRT) is a member of a large family of sodium-dependent neurotransmitter and amino acid transporters. The CRT is closely related to the gamma-aminobutyric acid (GABA) transporter, GAT-1, yet GABA is not an effective substrate for the CRT. The high resolution structure of a prokaryotic homologue, LeuT has revealed precise details of the substrate binding site for leucine (Yamashita, A., Singh, S. K., Kawate, T., Jin, Y., and Gouaux, E. (2005) Nature 437, 215-223). We have now designed mutations based on sequence comparisons of the CRT with GABA transporters and the LeuT structural template in an attempt to alter the substrate specificity of the CRT. Combinations of two or three amino acid substitutions at four selected positions resulted in the loss of creatine transport activity and gain of a specific GABA transport function. GABA transport by the "gain of function" mutants was sensitive to nipecotic acid, a competitive inhibitor of GABA transporters. Our results show LeuT to be a good structural model to identify amino acid residues involved in the substrate and inhibitor selectivity of eukaryotic sodium-dependent neurotransmitter and amino acid transporters. However, modification of the binding site alone appears to be insufficient for efficient substrate translocation. Additional residues must mediate the conformational changes required for the diffusion of substrate from the binding site to the cytoplasm.

  7. In Vitro Investigation of Self-Assembled Nanoparticles Based on Hyaluronic Acid-Deoxycholic Acid Conjugates for Controlled Release Doxorubicin: Effect of Degree of Substitution of Deoxycholic Acid

    Wen-Hao Wei

    2015-03-01

    Full Text Available Self-assembled nanoparticles based on a hyaluronic acid-deoxycholic acid (HD chemical conjugate with different degree of substitution (DS of deoxycholic acid (DOCA were prepared. The degree of substitution (DS was determined by titration method. The nanoparticles were loaded with doxorubicin (DOX as the model drug. The human cervical cancer (HeLa cell line was utilized for in vitro studies and cell cytotoxicity of DOX incorporated in the HD nanoparticles was accessed by the 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT assay. In addition, cellular uptake of fluorescently labeled nanoparticles was also investigated. An increase in the degree of deoxycholic acid substitution reduced the size of the nanoparticles and also enhanced their drug encapsulation efficiency (EE, which increased with the increase of DS. A higher degree of deoxycholic acid substitution also lead to a lower release rate and an initial burst release of doxorubicin from the nanoparticles. In summary, the degree of substitution allows the modulation of the particle size, drug encapsulation efficiency, drug release rate, and cell uptake efficiency of the nanoparticles. The herein developed hyaluronic acid-deoxycholic acid conjugates are a good candidate for drug delivery and could potentiate therapeutic formulations for doxorubicin–mediated cancer therapy.

  8. In vitro investigation of self-assembled nanoparticles based on hyaluronic acid-deoxycholic acid conjugates for controlled release doxorubicin: effect of degree of substitution of deoxycholic acid.

    Wei, Wen-Hao; Dong, Xue-Meng; Liu, Chen-Guang

    2015-03-31

    Self-assembled nanoparticles based on a hyaluronic acid-deoxycholic acid (HD) chemical conjugate with different degree of substitution (DS) of deoxycholic acid (DOCA) were prepared. The degree of substitution (DS) was determined by titration method. The nanoparticles were loaded with doxorubicin (DOX) as the model drug. The human cervical cancer (HeLa) cell line was utilized for in vitro studies and cell cytotoxicity of DOX incorporated in the HD nanoparticles was accessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. In addition, cellular uptake of fluorescently labeled nanoparticles was also investigated. An increase in the degree of deoxycholic acid substitution reduced the size of the nanoparticles and also enhanced their drug encapsulation efficiency (EE), which increased with the increase of DS. A higher degree of deoxycholic acid substitution also lead to a lower release rate and an initial burst release of doxorubicin from the nanoparticles. In summary, the degree of substitution allows the modulation of the particle size, drug encapsulation efficiency, drug release rate, and cell uptake efficiency of the nanoparticles. The herein developed hyaluronic acid-deoxycholic acid conjugates are a good candidate for drug delivery and could potentiate therapeutic formulations for doxorubicin-mediated cancer therapy.

  9. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

    Sanzo Miyazawa

    Full Text Available BACKGROUND: A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated. RESULTS: The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that

  10. 40 CFR 721.6181 - Fatty acid, reaction product with substituted oxirane, formaldehyde-phenol polymer glycidyl ether...

    2010-07-01

    ... substituted oxirane, formaldehyde-phenol polymer glycidyl ether, substituted proplyamine and...-phenol polymer glycidyl ether, substituted proplyamine and polyethylenepolyamines (generic). (a) Chemical... as fatty acid, reaction product with substituted oxirane, formaldehyde-phenol polymer glycidyl...

  11. The (non)malignancy of cancerous amino acidic substitutions.

    Talavera, David; Taylor, Martin S; Thornton, Janet M

    2010-02-15

    The process of natural selection acts both on individual organisms within a population and on individual cells within an organism as they develop into cancer. In this work, we have taken a first step toward understanding the differences in selection pressures exerted on the human genome under these disparate circumstances. Focusing on single amino acid substitutions, we have found that cancer-related mutations (CRMs) are frequent in evolutionarily conserved sites, whereas single amino acid polymorphisms (SAPs) tend to appear in sites having a more relaxed evolutionary pressure. Those CRMs classed as cancer driver mutations show greater enrichment for conserved sites than passenger mutations. Consistent with this, driver mutations are enriched for sites annotated as key functional residues and their neighbors, and are more likely to be located on the surface of proteins than expected by chance. Overall the pattern of CRM and polymorphism is remarkably similar, but we do see a clear signal indicative of diversifying selection for disruptive amino acid substitutions in the cancer driver mutations. The ultimate consequence of the appearance of those mutations must be advantageous for the tumor cell, leading to cell population-growth and migration events similar to those seen in natural ecosystems.

  12. QSBR study of substituted phenols and benzoic acids

    2003-01-01

    The biodegradability of 30 substituted phenols and benzoic acids was determined by BOD technique. The molecular weight (MW), heat of formation (Hf) and the energy of the highest occupied molecular orbital (EHOMO) of the studied compounds were calculated by the quantum chemical method MOPAC6.0-AM1. The quantitative structure-biodegradability relationships (QSBRs) were developed by the linear regression method and neural network approach, respectively. It has been shown that the neural network method is able to provide a superior fit to the training set data and test se t data and produce a lower prediction error than the linear regression method.

  13. 40 CFR 721.530 - Substituted aliphatic acid halide (generic name).

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Substituted aliphatic acid halide... Specific Chemical Substances § 721.530 Substituted aliphatic acid halide (generic name). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance substituted...

  14. Annonaceae substitution rates: a codon model perspective

    Lars Willem Chatrou

    2014-01-01

    Full Text Available The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

  15. Electroanalysis of amino acid substitutions in bioengineered acetylcholinesterase.

    Somji, Mehdi; Dounin, Vladimir; Muench, Susanne B; Schulze, Holger; Bachmann, Till T; Kerman, Kagan

    2012-12-01

    This study reports the electrochemical profiling of Nippostrongylus brasiliensis acetylcholinesterase (AChE) wild-type and mutant proteins. An irreversible oxidation signal of electro-active tyrosine (Y), tryptophan (W) and cysteine (C) residues in five mutant proteins along with the wild-type AChE were detected using square-wave voltammetry (SWV) on screen-printed carbon electrodes. Significant differences were observed in the W303L, T65Y and M301W substituted proteins showing a 25-35% higher peak current intensity compared to the Y349Y and F345Y mutants. It was predicted that AChE substituted with electrochemically active residues would produce the greatest signals and this trend was observed in the T65Y, M301W and Y349L mutants. However, conformational changes in the proteins structure as a result of the substitutions appeared to be most influential on peak current intensities. This was demonstrated by the W303L and F345Y mutant enzymes. The current intensity of W303L was greatest despite the removal of its electro-active W residue whereas the F345Y mutant had the lowest peak value despite the addition of an electro-active Y residue. The preliminary results of this study demonstrate that SWV provides a promising tool to probe the presence of electro-active amino acid residues on the surface of a protein produced through bioengineering.

  16. An effective synthesis of β-aryl substituted isotetronic acids via Suzuki coupling

    Huan Sheng Chen; Xia Ping Ma; Zhi Ming Li; Quan Rui Wang; Feng Gang Tao

    2008-01-01

    lsotetronic acids are of great agricultural and pharmacological relevance and occur in a number of natural products.A convenient synthetic pathway to β-aryl substituted isotetronic acid derivatives was developed via Suzuki cross-coupling of the corresponding β-bromo substituted isotetronic acid derivatives with arylboronic acids under palladium acetate catalysis.Good to excellent yields have been achieved.

  17. Synthesis and antiulcer activity studies of 2-(1′-iminothioimido substituted-1′-substituted phenylbenzoic acids

    Subudhi B

    2008-01-01

    Full Text Available Certain 2-(1′-iminothioimido substituted-1′-substituted phenybenzoic acids (P 1-9 were synthesized by reaction of phthalic anhydride with benzotriazole, 2-mercapto benzothiazole and 2-p-amino phenyl benzimidazole, respectively (A 1-3 followed by imine formation with Schiff bases of thiourea with salicylaldehyde, furfuraldehyde and 1-phenyl-3-methyl-5-pyrazolone. Antiulcer activity was evaluated using reduction in total acidity, free acidity and ulcer index as parameters. Compounds P 3 , P 6 , P 7 and P 9 (100 mg/kg showed significant (P< 0.001 antiulcer action compared to control and omeprazole (40 mg/kg.

  18. 40 CFR 721.2900 - Substituted aminobenzoic acid ester (generic name).

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Substituted aminobenzoic acid ester... Specific Chemical Substances § 721.2900 Substituted aminobenzoic acid ester (generic name). (a) Chemical... acid ester (PMN P-84-951) is subject to reporting under this section for the significant new...

  19. Amino acid-bile acid based molecules: extremely narrow surfactant nanotubes formed by a phenylalanine-substituted cholic acid.

    Travaglini, Leana; D'Annibale, Andrea; Schillén, Karin; Olsson, Ulf; Sennato, Simona; Pavel, Nicolae V; Galantini, Luciano

    2012-12-21

    An amino acid-substituted bile acid forms tubular aggregates with inner and outer diameters of about 3 and 6 nm. The diameters are unusually small for surfactant self-assembled tubes. The results enhance the spectrum of applications of supramolecular tubules and open up possibilities for investigating a novel class of biological amphiphiles.

  20. New Perspectives on Mechanisms of Decarboxylation in Hydrothermal Fluids from Studies of Substituted Phenylacetic Acids

    Glein, C. R.; Gould, I. R.; Lorance, E. D.; Shock, E. L.

    2011-12-01

    Decarboxylation reactions are thought to play a crucial role in transforming organic compounds in the deep carbon cycle [1]. Simple decarboxylation, defined as conversion of a carboxylic acid into an alkane and carbon dioxide, can turn substances of little economic value into ones of great value. Rates of decarboxylation of acetic acid and acetate at hydrothermal conditions have been reported [2], but no theory exists to rationalize those data. Without a theoretical model for how decarboxylations occur, it is risky to extrapolate available information to diverse geochemical conditions and molecular structures found in natural systems. We have been studying kinetics of decarboxylation of substituted phenylacetic acids and phenylacetates to gain insights into mechanisms of decarboxylation in water at high temperatures and pressures. These model compounds represent powerful tools for deciphering said mechanisms, as their patterns of reactivity reflect mechanistic details. Results from experiments performed at 300°C and 103 MPa suggest that simple decarboxylation of phenylacetic acids to toluenes follows an electrophilic substitution mechanism, featuring a benzyl anion as the key intermediate. This mechanism is consistent with the observed reactivity order of fluorophenylacetic acids: para (1) JACS 86, 404-409.

  1. 40 CFR 721.7770 - Alkylphenoxypoly(oxyethylene) sulfuric acid ester, substituted amine salt.

    2010-07-01

    ... acid ester, substituted amine salt. 721.7770 Section 721.7770 Protection of Environment ENVIRONMENTAL... ester, substituted amine salt. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as alkyl phenoxypoly(oxyethylene) sulfuric acid ester,...

  2. Bayesian selection of nucleotide substitution models and their site assignments.

    Wu, Chieh-Hsi; Suchard, Marc A; Drummond, Alexei J

    2013-03-01

    Probabilistic inference of a phylogenetic tree from molecular sequence data is predicated on a substitution model describing the relative rates of change between character states along the tree for each site in the multiple sequence alignment. Commonly, one assumes that the substitution model is homogeneous across sites within large partitions of the alignment, assigns these partitions a priori, and then fixes their underlying substitution model to the best-fitting model from a hierarchy of named models. Here, we introduce an automatic model selection and model averaging approach within a Bayesian framework that simultaneously estimates the number of partitions, the assignment of sites to partitions, the substitution model for each partition, and the uncertainty in these selections. This new approach is implemented as an add-on to the BEAST 2 software platform. We find that this approach dramatically improves the fit of the nucleotide substitution model compared with existing approaches, and we show, using a number of example data sets, that as many as nine partitions are required to explain the heterogeneity in nucleotide substitution process across sites in a single gene analysis. In some instances, this improved modeling of the substitution process can have a measurable effect on downstream inference, including the estimated phylogeny, relative divergence times, and effective population size histories.

  3. Antifungal activity of 4-substituted crotonic acid esters.

    Gershon, H; Shanks, L; Gawiak, D E

    1976-08-01

    Twenty-three 4-substituted crotonic acid esters were tested for antifungal activity against Candida albicans, Aspergillus niger, Mucor mucedo, and Trichophyton mentagrophytes. For the analogues of the methyl ester containing substituents in the 4 position, the following order of fungitoxicity was observed: I greater than Br greater than Cl greater than CH3S greater than CH3O greater than F=H. Of the homologues of the esters of the 4-iodo and 4-bromo compounds which included methyl, ethyl, n-propyl, n-butyl, n-pentyl, and n-hexyl, ethyl 4-iodocrotonate was most toxic to the four fungi at pH 7.0 in the presence of 10% beef serum (C. albicans, 18mug/ml, A. niger, 40 mug/ml, M. mucedo, 5 mug/ml, T. mentagrophytes, 4 mug/ml). It is believed that the mechanism of fungitoxicity is due, in part, to a nucleophilic reaction involving SH-containing compounds. This is based on the correlation of fungitoxicity with the order of leaving groups in the nucleophilic reaction and the protection against the toxicity of the test compounds to the fungi by cysteine and glutathione.

  4. Assessing the state of substitution models describing noncoding RNA evolution.

    Allen, James E; Whelan, Simon

    2014-01-01

    Phylogenetic inference is widely used to investigate the relationships between homologous sequences. RNA molecules have played a key role in these studies because they are present throughout life and tend to evolve slowly. Phylogenetic inference has been shown to be dependent on the substitution model used. A wide range of models have been developed to describe RNA evolution, either with 16 states describing all possible canonical base pairs or with 7 states where the 10 mismatched nucleotides are reduced to a single state. Formal model selection has become a standard practice for choosing an inferential model and works well for comparing models of a specific type, such as comparisons within nucleotide models or within amino acid models. Model selection cannot function across different sized state spaces because the likelihoods are conditioned on different data. Here, we introduce statistical state-space projection methods that allow the direct comparison of likelihoods between nucleotide models and 7-state and 16-state RNA models. To demonstrate the general applicability of our new methods, we extract 287 RNA families from genomic alignments and perform model selection. We find that in 281/287 families, RNA models are selected in preference to nucleotide models, with simple 7-state RNA models selected for more conserved families with shorter stems and more complex 16-state RNA models selected for more divergent families with longer stems. Other factors, such as the function of the RNA molecule or the GC-content, have limited impact on model selection. Our models and model selection methods are freely available in the open-source PHASE 3.0 software.

  5. Amino acid substitutions in random mutagenesis libraries: lessons from analyzing 3000 mutations.

    Zhao, Jing; Frauenkron-Machedjou, Victorine Josiane; Kardashliev, Tsvetan; Ruff, Anna Joëlle; Zhu, Leilei; Bocola, Marco; Schwaneberg, Ulrich

    2017-01-03

    The quality of amino acid substitution patterns in random mutagenesis libraries is decisive for the success in directed evolution campaigns. In this manuscript, we provide a detailed analysis of the amino acid substitutions by analyzing 3000 mutations of three random mutagenesis libraries (1000 mutations each; epPCR with a low-mutation and a high-mutation frequency and SeSaM-Tv P/P) employing lipase A from Bacillus subtilis (bsla). A comparison of the obtained numbers of beneficial variants in the mentioned three random mutagenesis libraries with a site saturation mutagenesis (SSM) (covering the natural diversity at each amino acid position of BSLA) concludes the diversity analysis. Seventy-six percent of the SeSaM-Tv P/P-generated substitutions yield chemically different amino acid substitutions compared to 64% (epPCR-low) and 69% (epPCR-high). Unique substitutions from one amino acid to others are termed distinct amino acid substitutions. In the SeSaM-Tv P/P library, 35% of all theoretical distinct amino acid substitutions were found in the 1000 mutation library compared to 25% (epPCR-low) and 26% (epPCR-high). Thirty-six percent of distinct amino acid substitutions found in SeSaM-Tv P/P were unobtainable by epPCR-low. Comparison with the SSM library showed that epPCR-low covers 15%, epPCR-high 18%, and SeSaM-Tv P/P 21% of obtainable beneficial amino acid positions. In essence, this study provides first insights on the quality of epPCR and SeSaM-Tv P/P libraries in terms of amino acid substitutions, their chemical differences, and the number of obtainable beneficial amino acid positions.

  6. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size.

    Ohta, T

    1993-01-01

    The number of amino acid replacement substitutions and that of synonymous substitutions are examined by using DNA sequences of the Adh locus of Drosophila. The ratio of replacement to synonymous substitutions is higher in sequence comparisons between species than in polymorphisms within species. The ratio for the between-species comparisons is highest in the Hawaiian group and lowest in the obscura group. These observations suggest that amino acid substitutions are facilitated by small population size. The result is in accord with the nearly neutral theory of molecular evolution. PMID:8506297

  7. Structural consequences of amino acid substitutions causing Tay-Sachs disease.

    Ohno, Kazuki; Saito, Seiji; Sugawara, Kanako; Sakuraba, Hitoshi

    2008-08-01

    To determine the structural changes in the alpha-subunit of beta-hexosaminidase due to amino acid substitutions causing Tay-Sachs disease, we built structural models of mutant alpha-subunits resulting from 33 missense mutations (24 infantile and 9 late-onset), and analyzed the influence of each amino acid replacement on the structure by calculating the number of atoms affected and determining the solvent-accessible surface area of the corresponding amino acid residue in the wild-type alpha-subunit. In the infantile Tay-Sachs group, the number of atoms influenced by a mutation was generally larger than that in the late-onset Tay-Sachs group in both the main chain and the side chain, and residues associated with the mutations found in the infantile Tay-Sachs group tended to be less solvent-accessible than those in the late-onset Tay-Sachs group. Furthermore, color imaging determined the distribution and degree of the structural changes caused by representative amino acid substitutions, and that there were also differences between the infantile and late-onset Tay-Sachs disease groups. Structural study is useful for elucidating the basis of Tay-Sachs disease.

  8. Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted alpha-methoxystyrenes and substituted acetic acids.

    Wong, Kin-Yiu; Richard, John P; Gao, Jiali

    2009-10-01

    Primary kinetic isotope effects (KIEs) on a series of carboxylic acid-catalyzed protonation reactions of aryl-substituted alpha-methoxystyrenes (X-1) to form oxocarbenium ions have been computed using the second-order Kleinert variational perturbation theory (KP2) in the framework of Feynman path integrals (PI) along with the potential energy surface obtained at the B3LYP/6-31+G(d,p) level. Good agreement with the experimental data was obtained, demonstrating that this novel computational approach for computing KIEs of organic reactions is a viable alternative to the traditional method employing Bigeleisen equation and harmonic vibrational frequencies. Although tunneling makes relatively small contributions to the lowering of the free energy barriers for the carboxylic acid catalyzed protonation reaction, it is necessary to include tunneling contributions to obtain quantitative estimates of the KIEs. Consideration of anharmonicity can further improve the calculated KIEs for the protonation of substituted alpha-methoxystyrenes by chloroacetic acid, but for the reactions of the parent and 4-NO(2) substituted alpha-methoxystyrene with substituted carboxylic acids, the correction of anharmonicity overestimates the computed KIEs for strong acid catalysts. In agreement with experimental findings, the largest KIEs are found in nearly ergoneutral reactions, DeltaG(o) approximately 0, where the transition structures are nearly symmetric and the reaction barriers are relatively low. Furthermore, the optimized transition structures are strongly dependent on the free energy for the formation of the carbocation intermediate, that is, the driving force DeltaG(o), along with a good correlation of Hammond shift in the transition state structure.

  9. Photo-Reversible Supramolecular Hydrogels Assembled by α-Cyclodextrin and Azobenzene Substituted Poly(acrylic acid)s

    Wang, Mingwei; Zhang, Xiaojun; Li, Li; Wang, Junyou; Wang, Jie; Ma, Jun; Yuan, Zhenyu; Lincoln, Stephen F.; Guo, Xuhong

    2016-01-01

    Photo-reversible supramolecular hydrogels based on the mixture of α-cyclodextrin (α-CD) and azobenzene (Azo) substituted poly(acrylic acid) s were prepared. Effects of substitution degree of Azo, polymer concentration and tethered chain length on the reversible sol-gel transition of these mixture

  10. Between peptides and bile acids: self-assembly of phenylalanine substituted cholic acids.

    Travaglini, Leana; D'Annibale, Andrea; di Gregorio, Maria Chiara; Schillén, Karin; Olsson, Ulf; Sennato, Simona; Pavel, Nicolae V; Galantini, Luciano

    2013-08-01

    Biocompatible molecules that undergo self-assembly are of high importance in biological and medical applications of nanoscience. Peptides and bile acids are among the most investigated due to their ability to self-organize into many different, often stimuli-sensitive, supramolecular structures. With the aim of preparing molecules mixing the aggregation properties of bile acid and amino acid-based molecules, we report on the synthesis and self-association behavior of two diastereomers obtained by substituting a hydroxyl group of cholic acid with a l-phenylalanine residue. The obtained molecules are amphoteric, and we demonstrate that they show a pH-dependent self-assembly. Both molecules aggregate in globular micelles at high pH, whereas they form tubular superstructures under acid conditions. Unusual narrow nanotubes with outer and inner cross-section diameters of about 6 and 3 nm are formed by the derivatives. The diasteroisomer with α orientation of the substituent forms in addition a wider tubule (17 nm cross-section diameter). The ability to pack in supramolecular tubules is explained in terms of a wedge-shaped bola-form structure of the derivatives. Parallel or antiparallel face-to-face dimers are hypothesized as fundamental building blocks for the formation of the narrow and wide nanotubes, respectively.

  11. Synthesis and characterization of some N-substituted amides of salicylic acid

    Lupea Xenia Alfa; Padure Mirabela

    2003-01-01

    The synthesis of some N-substituted aromatic amides in the salicylic acid series was achieved, by direct reaction between primary amines and salicylic acid in inert organic solvent, in the presence of PCl3. The compounds that were obtained, partially not described in literature, were characterized by chemical-physical methods.

  12. Synthesis and characterization of some N-substituted amides of salicylic acid

    Lupea Xenia Alfa

    2003-01-01

    Full Text Available The synthesis of some N-substituted aromatic amides in the salicylic acid series was achieved, by direct reaction between primary amines and salicylic acid in inert organic solvent, in the presence of PCl3. The compounds that were obtained, partially not described in literature, were characterized by chemical-physical methods.

  13. Liquid Membrane Transport Behavior of Functional Substituted Crown Ethers for Amino Acids

    2002-01-01

    Three functional substituted crown ethers were synthesized as liquid membrane transport carriers for amino acids. The result obtained shows that this kind of ditopic ligands can transport sodium salt of amino acids in good rate value especially the one with two pyridinyl groups as binding site outside the macrocycle.

  14. Binding of ring-substituted indole-3-acetic acids to human serum albumin.

    Soskić, Milan; Magnus, Volker

    2007-07-01

    The plant hormone, indole-3-acetic acid (IAA), and its ring-substituted derivatives have recently attracted attention as promising pro-drugs in cancer therapy. Here we present relative binding constants to human serum albumin for IAA and 34 of its derivatives, as obtained using the immobilized protein bound to a support suitable for high-performance liquid chromatography. We also report their octanol-water partition coefficients (logK(ow)) computed from retention data on a C(18) coated silica gel column. A four-parameter QSPR (quantitative structure-property relationships) model, based on physico-chemical properties, is put forward, which accounts for more than 96% of the variations in the binding affinities of these compounds. The model confirms the importance of lipophilicity as a global parameter governing interaction with serum albumin, but also assigns significant roles to parameters specifically related to the molecular topology of ring-substituted IAAs. Bulky substituents at ring-position 6 increase affinity, those at position 2 obstruct binding, while no steric effects were noted at other ring-positions. Electron-withdrawing substituents at position 5 enhance binding, but have no obvious effect at other ring positions.

  15. Heteropoly acids of the Keggin type with N-substitutedβ-amminoethylphosphonic acids as coordinate center

    2001-01-01

    Organophosphorus-heteropolytungstic acids of 1 : 12 of P/W ratio, with N-substituted 2-amminoethylphosphonic acids R2R'N+CH2CH2PO3H-(R = R' = H; R = Me, R' = H; R = R' = Me;R = H, R' = Me2CH; R = H, R' = CH3(CH2)2CH2) as coordinate centers were prepared, and char-acterized by means of elemental analysis, IR, UV spectroscopy, TG and DSC thermal analysis.The results indicate that these organophosphorous-HPAs possess Keggin type structure, and theirstoichiometric formulation is R2R'N+CH2CH2PO3H-·W12O36 ·nH2O. The organic side chain with theammino-group R2R'N+CH2CH2-and the phosphono-group-PO3H-participate altogether in the for-mation of the primary structure of the heteropoly anion. In other words, the entirety of eachcompound R2R'N+CH2CH2PO3H-is as the core or coordinate center of the heteropoly anions. Thenumber of crystal water in the HPA was affected obviously by the N-substituents of the organo-phosphonic acids.

  16. Theoretical Study of 1,3-Dipolar Cycloaddition of Hydrazoic Acid to Substituted Ynamines

    Xiaofang Chen; Kun Yang; Keli Han

    2009-01-01

    The 1,3-dipolar cycloaddition reactions of various substituted ynamines with hydrazoic acid were theoretically investigated with the high-accuracy CBS-QB3 method. Two regioisomers,4-amine, and 5-amine substituted adducts, were obtained, with the former as the preferred yield. This regioselectivity is rationalized by the frontier molecular orbital theory. The reactivity and synchronicity are enhanced with the increase of the electron-withdrawing character of the substitute on ynamine fragment. The calculations also show that the effect of solvent increases the activation energy, and the reaction becomes even harder in polar solvent.

  17. Theoretical Study of 1,3-Dipolar Cycloaddition of Hydrazoic Acid to Substituted Ynamines

    Chen, Xiao-fang; Yang, Kun; Han, Ke-li

    2009-04-01

    The 1,3-dipolar cycloaddition reactions of various substituted ynamines with hydrazoic acid were theoretically investigated with the high-accuracy CBS-QB3 method. Two regioisomers, 4-amine, and 5-amine substituted adducts, were obtained, with the former as the preferred yield. This regioselectivity is rationalized by the frontier molecular orbital theory. The reactivity and synchronicity are enhanced with the increase of the electron-withdrawing character of the substitute on ynamine fragment. The calculations also show that the effect of solvent increases the activation energy, and the reaction becomes even harder in polar solvent.

  18. Aggregation and metal ion extraction properties of novel, silicon-substituted alkylenediphosphonic acids.

    McAlister, D. R.; Dietz, M. L.; Chiarizia, R.; Herlinger, A. W.

    2001-05-10

    In conjunction with efforts to develop novel actinide extractants exhibiting solubility in supercritical carbon dioxide, the effect of adding silicon-based functionalities to diphosphonic acids has been investigated. Specifically, a series of silyl-substituted diphosphonic acids has been prepared and characterized, and their aggregation and metal ion extraction properties compared with alkyl-substituted diphosphonic acids, reagents previously demonstrated to be effective extractants of actinides from acidic aqueous media into various organic solvents. In addition, the influence of the number of methylene groups bridging the phosphorus atoms of the diphosphonic acids on their extraction behavior has been investigated. Variations in the extraction behavior of the compounds arising from differences in the number of bridging methylene groups have been shown to be attributable to a combination of factors, in particular, the aggregation state of the ligand, the size of the chelate rings formed upon complexation, the basicity of the phosphoryl group and the relative acidities of the ligands.

  19. The effect of amino acid deletions and substitutions in the longest loop of GFP

    Gaytán Paul

    2007-06-01

    Full Text Available Abstract Background The effect of single and multiple amino acid substitutions in the green fluorescent protein (GFP from Aequorea victoria has been extensively explored, yielding several proteins of diverse spectral properties. However, the role of amino acid deletions in this protein -as with most proteins- is still unknown, due to the technical difficulties involved in generating combinatorial in-phase amino acid deletions on a target region. Results In this study, the region I129-L142 of superglo GFP (sgGFP, corresponding to the longest loop of the protein and located far away from the central chromophore, was subjected to a random amino acid deletion approach, employing an in-house recently developed mutagenesis method termed Codon-Based Random Deletion (COBARDE. Only two mutants out of 16384 possible variant proteins retained fluorescence: sgGFP-Δ I129 and sgGFP-Δ D130. Interestingly, both mutants were thermosensitive and at 30°C sgGFP-Δ D130 was more fluorescent than the parent protein. In contrast with deletions, substitutions of single amino acids from residues F131 to L142 were well tolerated. The substitution analysis revealed a particular importance of residues F131, G135, I137, L138, H140 and L142 for the stability of the protein. Conclusion The behavior of GFP variants with both amino acid deletions and substitutions demonstrate that this loop is playing an important structural role in GFP folding. Some of the amino acids which tolerated any substitution but no deletion are simply acting as "spacers" to localize important residues in the protein structure.

  20. Quantum Chemical Benchmarking, Validation, and Prediction of Acidity Constants for Substituted Pyridinium Ions and Pyridinyl Radicals.

    Keith, John A; Carter, Emily A

    2012-09-11

    Sensibly modeling (photo)electrocatalytic reactions involving proton and electron transfer with computational quantum chemistry requires accurate descriptions of protonated, deprotonated, and radical species in solution. Procedures to do this are generally nontrivial, especially in cases that involve radical anions that are unstable in the gas phase. Recently, pyridinium and the corresponding reduced neutral radical have been postulated as key catalysts in the reduction of CO2 to methanol. To assess practical methodologies to describe the acid/base chemistry of these species, we employed density functional theory (DFT) in tandem with implicit solvation models to calculate acidity constants for 22 substituted pyridinium cations and their corresponding pyridinyl radicals in water solvent. We first benchmarked our calculations against experimental pyridinium deprotonation energies in both gas and aqueous phases. DFT with hybrid exchange-correlation functionals provide chemical accuracy for gas-phase data and allow absolute prediction of experimental pKas with unsigned errors under 1 pKa unit. The accuracy of this economical pKa calculation approach was further verified by benchmarking against highly accurate (but very expensive) CCSD(T)-F12 calculations. We compare the relative importance and sensitivity of these energies to selection of solvation model, solvation energy definitions, implicit solvation cavity definition, basis sets, electron densities, model geometries, and mixed implicit/explicit models. After determining the most accurate model to reproduce experimentally-known pKas from first principles, we apply the same approach to predict pKas for radical pyridinyl species that have been proposed relevant under electrochemical conditions. This work provides considerable insight into the pitfalls using continuum solvation models, particularly when used for radical species.

  1. Banana-shaped molecules derived from substituted isophthalic acids

    H T Nguyen; J P Bedel; J C Rouillon; J P Marcerou; M F Achard

    2003-08-01

    In this paper we present a review of five-rings banana-shaped molecules derived from isophthalic acids. This study deals with about a hundred compounds and most of them have not been published. By a combination of several linking groups and different selected substituents either on the outer rings or on the central core, several mesophases with switching properties are induced. The study of homologous series underlines the importance of the length and nature of the terminal chains. X-ray analysis reveals several new structures.

  2. Substitution of trans fatty acids in foods on the Danish market

    Bysted, Anette; Mikkelsen, Aase Ærendahl; Leth, Torben

    2009-01-01

    , in 68% of the products (e.g. sweets, cakes and cookies as well as fast food such as pie and tortilla), IP-TFA were mainly substituted with saturated fatty acids (SFA). In some cases, the SFA source was coconut fat, whereas in other products, palm oil was added instead of partially hydrogenated oils...

  3. 40 CFR 721.1875 - Boric acid, alkyl and substituted alkyl esters (generic name).

    2010-07-01

    ... alkyl esters (generic name). 721.1875 Section 721.1875 Protection of Environment ENVIRONMENTAL... esters (generic name). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance boric acid, alkyl and substituted alkyl esters (PMN P-86-1252) is subject to...

  4. Mechanical Models of the Dynamics of Vitreous Substitutes

    Pralits, Jan O.; Repetto, Rodolfo; Romano, Mario R.

    2014-01-01

    We discuss some aspects of the fluid dynamics of vitreous substitutes in the vitreous chamber, focussing on the flow induced by rotations of the eye bulb. We use simple, yet not trivial, theoretical models to highlight mechanical concepts that are relevant to understand the dynamics of vitreous substitutes and also to identify ideal properties for vitreous replacement fluids. We first recall results by previous authors, showing that the maximum shear stress on the retina grows with increasing viscosity of the fluid up to a saturation value. We then investigate how the wall shear stress changes if a thin layer of aqueous humour is present in the vitreous chamber, separating the retina from the vitreous replacement fluid. The theoretical predictions show that the existence of a thin layer of aqueous is sufficient to substantially decrease the shear stress on the retina. We finally discuss a theoretical model that predicts the stability conditions of the interface between the aqueous and a vitreous substitute. We discuss the implications of this model to understand the mechanisms leading to the formation of emulsion in the vitreous chamber, showing that instability of the interface is possible in a range of parameters relevant for the human eye. PMID:25147810

  5. Mechanical Models of the Dynamics of Vitreous Substitutes

    Krystyna Isakova

    2014-01-01

    Full Text Available We discuss some aspects of the fluid dynamics of vitreous substitutes in the vitreous chamber, focussing on the flow induced by rotations of the eye bulb. We use simple, yet not trivial, theoretical models to highlight mechanical concepts that are relevant to understand the dynamics of vitreous substitutes and also to identify ideal properties for vitreous replacement fluids. We first recall results by previous authors, showing that the maximum shear stress on the retina grows with increasing viscosity of the fluid up to a saturation value. We then investigate how the wall shear stress changes if a thin layer of aqueous humour is present in the vitreous chamber, separating the retina from the vitreous replacement fluid. The theoretical predictions show that the existence of a thin layer of aqueous is sufficient to substantially decrease the shear stress on the retina. We finally discuss a theoretical model that predicts the stability conditions of the interface between the aqueous and a vitreous substitute. We discuss the implications of this model to understand the mechanisms leading to the formation of emulsion in the vitreous chamber, showing that instability of the interface is possible in a range of parameters relevant for the human eye.

  6. Synthesis and Antimicrobial Activity of 2-[4-(Substituted Benzylidenamino-5-(Substituted Phenoxymethyl-4H-1,2,4-Triazol-3-yl thio] Acetic Acid Derivatives

    R. D. Hunashal

    2012-01-01

    Full Text Available 2-[4-(substituted benzylidenamino-5-(substituted phenoxymethyl-4H-1,2,4-triazol-3-yl thio] acetic acid (3a-j derivatives have been synthesized by the reaction between 4-(substituted benzylidenamino-5-(substituted phenoxymethyl-2H-1,2,4-triazol-3(4H-thiones (2a-j and chloroacetic acid containing catalytic amount of pyridine. All these compounds were screened for antimicrobial activity. The compounds 3h and 3j exhibited good antifungal activity against A. niger, C. Neoformans, and A. fumigatus at MIC of 0.25 μg/ml compared to standard drug fluconazole at MIC of 1 μg/mL.

  7. A Quantitative Structure-Activity Relationship and Molecular Modeling Study on a Series of Heteroaryl- and Heterocyclyl-Substituted Imidazo[1,2-a]Pyridine Derivatives Acting as Acid Pump Antagonists

    Neeraj Agarwal

    2013-01-01

    Full Text Available A quantitative structure-activity relationship (QSAR and molecular docking study has been performed on a series of heteroaryl- and heterocyclyl-substituted imidazo[1,2-a]pyridine derivatives acting as acid pump antagonists in order to have a better understanding of the mechanism of H+/K+-ATPase inhibition. The QSAR study shows a significant correlation of activity with Global Topological Charge Indices (GTCI of the compounds and the hydrophobic constant of some substituents, indicating that the charge transfer within the molecule and the hydrophobic property of some substituents will be the controlling factor of the activity of these compounds and that there can be dispersion interaction between the molecules and the receptor, where some substituents may have hydrophobic interaction, too. Based on this correlation some new compounds with higher potency have been predicted and their docking study has been performed to see if they can have better interaction with the receptor. The ADME properties of these predicted compounds have also been reported that follow Lipinski’s rule of five.

  8. The influence of the solvent on organic reactivity. Part II. Hydroxylic solvent effects on the reaction rates of diazodiphenylmethane with 2-(2-substituted cyclohex-1-enylacetic and 2-(2-substituted phenylacetic acids

    VERA V. KRSTIC

    2004-09-01

    Full Text Available The rate constants for the reaction of diazodiphenylmethane with 2-(2-substituted cyclohex-1-enylacetic acids and 2-(2-substituted phenylacetic acids, previously determined in seven hydroxylic solvents, were correlated using the total solvatochromic equation, of the form: log k = log k0 + sp* + aa + bb, the two-parameter model, log log k = log k0 + sp* + aa, and a single parameter model k = log k0 + sp* + bb, where p* is a measure of the solvent polarity, b represents the scale of solvent hydrogen bond acceptor basicities and a represents the scale of solvent hydrogen bond donor acidities. The correlations of the kinetic data were carried out by means of multiple linear regression analysis and the solvent effects on the reaction rates were analysed in terms of initial state and transition state contributions.

  9. Phenylalanine Aminomutase-Catalyzed Addition of Ammonia to Substituted Cinnamic Acids : a Route to Enantiopure alpha- and beta-Amino Acids

    Szymanski, Wiktor; Wu, Bian; Weiner, Barbara; de Wildeman, Stefaan; Feringa, B.L.; B. Janssen, Dick

    2009-01-01

    An approach is described for the synthesis of aromatic alpha- and beta-amino acids that Uses phenylalanine aminomutase to catalyze a highly enantioselective addition of ammonia to substituted cinnamic acids. The reaction has a broad scope and yields Substituted alpha- and beta-phenylalanines with ex

  10. Development of a stratum corneum substitute for in vitro percutaneous penetration studies : a skin barrier model comprising synthetic stratum corneum lipids

    Jager, Miranda Wilhelmina de

    2006-01-01

    The research outlined in this thesis was focused on the development of a skin barrier model, which can substitute for stratum corneum in diffusion studies. This so-called stratum corneum substitute (SCS) was prepared with reconstituted SC lipids (cholesterol, free fatty acids and ceramides) on a por

  11. Heteropoly acids of the Keggin type with N-substituted

    FU; Xiangkai

    2001-01-01

    [1]Hartman, P., Perdok, G., On the relationship between structure and morphology of crystals, Acta Cryst., 1955, 8: 525-529.[2]Woensdregt, C. F., Computation of surface of energies in an electrostatic point charge model, Ⅱ. Application to zircon (ZrSiO4), Phys. Chem. Minerals, 1992, 19: 417-423.[3]Kern, R., The equilibrium form of a crystal, in Morphology of Crystal (ed. Sunnagawa, I.), Tokyo: Terra Scientific Publishing Company, 1970, 77-206.[4]Machenzie, J. K., Moore, J. W., Nickolas, J. F., Bond broken at atomically flat crystal surface, I. Face-centered and body-centered cubic crystal, J. Phys. Chem. Solids, 1962, 23: 185-196.[5]?. Machenzie, J. K., Nicholas, J. F., Bond broken at atomically flat crystal surface, ?. Crystals containing many atoms in a primitive unit cell, J. Phys. Chem. Solids, 1962, 23: 197-205.[6]Hazen, R. M., Finger, L. W., Crystal structure and compressibility of zircon at high pressure, Am. Mineral, 1979, 64:196-201.[7]Pupin, J. P., Zircon and granite petrology, Contrib. Mineral Petrol., 1980, 73: 207-220.[8]Wang, X., Kienast, J. R., Morphology and geochemistry of zircon: a case study on zircon from the microgranitoid enclaves,Science in China, Series D, 1999, 42(5): 544-552.[9]Wang, X., Li, W. X., Discovery of the { 211 }-type of zircon and its petrogenetic implication, Chinese Sci. Bull., 2001 (inpress).[10]Wang, X., Quantitative description of zircon morphology and its dynamics analysis, Science in China, Series D, 1998,41(4): 422-428.

  12. Cytotoxic conjugates of betulinic acid and substituted triazoles prepared by Huisgen Cycloaddition from 30-azidoderivatives

    Sidova, Veronika; Zoufaly, Pavel; Pokorny, Jan; Dzubak, Petr; Hajduch, Marian; Popa, Igor

    2017-01-01

    In this work, we describe synthesis of conjugates of betulinic acid with substituted triazoles prepared via Huisgen 1,3-cycloaddition. All compounds contain free 28-COOH group. Allylic bromination of protected betulinic acid by NBS gave corresponding 30-bromoderivatives, their substitution with sodium azides produced 30-azidoderivatives and these azides were subjected to CuI catalysed Huisgen 1,3-cycloaddition to give the final conjugates. Reactions had moderate to high yields. All new compounds were tested for their in vitro cytotoxic activities on eight cancer and two non-cancer cell lines. The most active compounds were conjugates of 3β-O-acetylbetulinic acid and among them, conjugate with triazole substituted by benzaldehyde 9b was the best with IC50 of 3.3 μM and therapeutic index of 9.1. Five compounds in this study had IC50 below 10 μM and inhibited DNA and RNA synthesis and caused block in G0/G1 cell cycle phase which is highly similar to actinomycin D. It is unusual that here prepared 3β-O-acetates were more active than compounds with the free 3-OH group and this suggests that this set may have common mechanism of action that is different from the mechanism of action of previously known 3β-O-acetoxybetulinic acid derivatives. Benzaldehyde type conjugate 9b is the best candidate for further drug development. PMID:28158265

  13. Solid Phase Synthesis of 2-Substituted 1,3-Oxazin-6-ones Using Resin-bound Cyclic Malonic Acid Ester

    LIU, Zhan-Xiang(刘占祥); RUAN, Xiu-Xiu(阮秀秀); HUANG, Xian(黄宪)

    2004-01-01

    A facile solid phase synthesis of 2-substituted 1,3-oxazin-6-ones using polymer-supported Meldrum's acid has been reported. Reaction of the resin-bound cyclic malonic acid ester with triethyl orthoformate and subsequent double substitution with amide, afforded the corresponding polymer-supported acylaminomethylene cyclic malonic acid ester, which upon thermal treatment led to 1, 3-oxazin-6-ones in good yields and with high purity.

  14. Synthesis and Structural Characterization of 1- and 2-Substituted Indazoles: Ester and Carboxylic Acid Derivatives

    Isabel Bento

    2006-11-01

    Full Text Available A series of indazoles substituted at the N-1 and N-2 positions with ester-containing side chains -(CH2nCO2R of different lengths (n = 0-6, 9, 10 are described.Nucleophilic substitution reactions on halo esters (X(CH2nCO2R by 1H-indazole inalkaline solution lead to mixtures of N-1 and N-2 isomers, in which the N-1 isomerpredominates. Basic hydrolysis of the ester derivatives allowed the synthesis of thecorresponding indazole carboxylic acids. All compounds were fully characterised bymultinuclear NMR and IR spectroscopies, MS spectrometry and elemental analysis; theNMR spectroscopic data were used for structural assignment of the N-1 and N-2 isomers.The molecular structure of indazol-2-yl-acetic acid (5b was determined by X-raydiffraction, which shows a supramolecular architecture involving O2-H...N1intermolecular hydrogen bonds.

  15. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1 Viruses.

    William T Harvey

    2016-04-01

    Full Text Available Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1 virus isolates (1997-2009 and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens.

  16. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses.

    Harvey, William T; Benton, Donald J; Gregory, Victoria; Hall, James P J; Daniels, Rodney S; Bedford, Trevor; Haydon, Daniel T; Hay, Alan J; McCauley, John W; Reeve, Richard

    2016-04-01

    Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997-2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens.

  17. Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains

    Branislava Gemovic

    2013-01-01

    Full Text Available There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM, a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

  18. Thermodynamics of axial substitution and kinetics of reactions with amino acids for the paddlewheel complex tetrakis(acetato)chloridodiruthenium(II,III).

    Santos, Rodrigo L S R; van Eldik, Rudi; de Oliveira Silva, Denise

    2012-06-18

    The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru(2)(CH(3)COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters ΔH°, ΔS°, and ΔV° were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru(2) substituted species. The results revealed that the [Ru(2)(CH(3)COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.

  19. Anticancer Activities of Substituted Cinnamic Acid Phenethyl Esters on Human Cancer Cell Lines

    LIShu-chun; LIHui; ZHANGFa; LIZhong-jun; CUIJing-rong

    2003-01-01

    Caffeic acid phenethyl ester (CAPE) and sixteen substituted cinnamic acid phenethyl esters were prepared via conventional procedures in order to test their in vitro anticancer activities by either MTT assay or SRB assay on six different human cancer cell lines. The results indicated that in the concentration of 10μmol·L-1 the lead compmuM CAPE possessed anficancer activities against human HL-60, Bel-7402, and Hela cell lines, and two other compounds possessed potent anticancer activities against Bel-7402 and Hela cell lines.

  20. Electrochemical oxidation of substituted benzylamines in aquo-acetic acid medium: substituent and solvent effects

    A Thirumoorthi; K P Elango

    2007-07-01

    Electrochemical oxidation of nine para- and meta-substituted benzylamines in varying mole fractions of acetic acid in water has been investigated in the presence of 0.1 M sulphuric acid as supporting electrolyte. The oxidation potentials correlate well with Hammett’s substituent constants affording negative reaction constants. The correlation of potential values with macroscopic solvent parameters is non-linear suggesting that the operation of both specific and non-specific solvent-solvent-solute interaction mechanisms. Multiple correlation analysis of the experimental data with Kamlet-Taft solvatochromic parameters is employed.

  1. Evaluating EDTA as a substitute for phosphoric acid-etching of enamel and dentin.

    Imbery, Terence A; Kennedy, Matthew; Janus, Charles; Moon, Peter C

    2012-01-01

    Matrix metalloproteinases (MMPs) are proteolytic enzymes released when dentin is acid-etched. The enzymes are capable of destroying unprotected collagen fibrils that are not encapsulated by the dentin adhesive. Chlorhexidine applied after etching inhibits the activation of released MMPs, whereas neutral ethylenediamine tetra-acetic acid (EDTA) prevents the release of MMPs. The purpose of this study was to determine if conditioning enamel and dentin with EDTA can be a substitute for treating acid-etching enamel and dentin with chlorhexidine. A column of composite resin was bonded to enamel and dentin after conditioning. Shear bond strengths were evaluated after 48 hours and after accelerated aging for three hours in 12% sodium hypochlorite. Shear bond strengths ranged from 15.6 MP a for accelerated aged EDTA enamel specimens to 26.8 MPa for dentin conditioned with EDTA and tested after 48 hours. A three-way ANOVA and a Tukey HSD test found statistically significant differences among the eight groups and the three independent variables (P EDTA was successfully substituted for phosphoric acid-etched enamel and dentin treated with chlorhexidine. Interactions of conditioning agent and aging were significant for dentin but not for enamel. In an effort to reduce the detrimental effects of MMPs, conditioning enamel and dentin with EDTA is an alternative to treating acid-etched dentin and enamel with chlorhexidine.

  2. Brønsted Acid-Catalyzed Direct Substitution of 2-Ethoxytetrahydrofuran with Trifluoroborate Salts

    Kayla M. Fisher

    2016-06-01

    Full Text Available Metal-free transformations of organotrifluoroborates are advantageous since they avoid the use of frequently expensive and sensitive transition metals. Lewis acid-catalyzed reactions involving potassium trifluoroborate salts have emerged as an alternative to metal-catalyzed protocols. However, the drawbacks to these methods are that they rely on the generation of unstable boron dihalide species, thereby resulting in low functional group tolerance. Recently, we discovered that in the presence of a Brønsted acid, trifluoroborate salts react rapidly with in situ generated oxocarbenium ions. Here, we report Brønsted acid-catalyzed direct substitution of 2-ethoxytetrahydrofuran using potassium trifluoroborate salts. The reaction occurs when tetrafluoroboric acid is used as a catalyst to afford functionalized furans in moderate to excellent yields. A variety of alkenyl- and alkynyltrifluoroborate salts readily participate in this transformation.

  3. Synthesis and evaluation of 4-substituted semicarbazones of levulinic acid for anticonvulsant activity

    AGGARWAL Navneet; MISHRA Pradeep

    2005-01-01

    Objective: A series of 4-aryl substituted semicarbazones of levulinic acid (4-oxo pentanoic acid) was designed and synthesized to meet the structural requirements essential for anticonvulsant activity. Methods: All the compounds were evaluated for anticonvulsant activity. Anticonvulsant activity was determined after intraperitoneal (i.p.) administration to mice by maximal electroshock (MES) and subcutaneous metrazol (ScMet) induced seizure methods and minimal motor impairment was determined by rotorod test. Results: A majority of the compounds exhibited significant anticonvulsant activity after intraperitoneal administration. In the present study 4-(4'-fluoro phenyl) levulinic acid semicarbazone emerged as the most active molecule, showing broad spectrum of activity with low neurotoxicity. Unsubstituted levulinic acid semicarbazone was found to be inactive in all the screens. Conclusion: The results obtained validate the hypothesis that presence of an aryl group near the semicarbazone moiety is essential for anticonvulsant activity. The results also indicate that the hydrophilic-hydrophobic site can accommodate hydrophilic groups.

  4. Molecular pharmacology of 4-substituted glutamic acid analogues at ionotropic and metabotropic excitatory amino acid receptors

    Bräuner-Osborne, Hans; Nielsen, B; Stensbøl, T B;

    1997-01-01

    using rat brain ionotropic glutamate receptors, and in functional assays using cloned metabotropic glutamate (mGlu) receptors. As a notable result of these studies, (2S,4R)-4-methylglutamic acid and (2S,4S)-4-methylglutamic acid were shown to be selective for kainic acid receptors and mGlu receptors......The pharmacology of (2S,4R)-4-methylglutamic acid, (2S,4S)-4-methylglutamic acid and (S)- and (R)-4-methyleneglutamic acids (obtained in high chemical and enantiomeric purity from racemic 4-methyleneglutamic acid by chiral HPLC using a Crownpak CR(+) column), was examined in binding experiments...... (subtypes 1alpha and 2), respectively, whereas (S)-4-methyleneglutamic acid showed high but rather non-selective affinity for the (RS)-2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA), kainic acid, NMDA and mGlu receptors (subtypes 1alpha and 2). Although none of the compounds were specific...

  5. Vapor Phase Dehydration of Glycerol to Acrolein Over SBA-15 Supported Vanadium Substituted Phosphomolybdic Acid Catalyst.

    Viswanadham, Balaga; Srikanth, Amirineni; Kumar, Vanama Pavan; Chary, Komandur V R

    2015-07-01

    Vapor phase dehydration of glycerol to acrolein was investigated over heteropolyacid (HPA) catalysts containing vanadium substituted phosphomolybdic acid (H4PMo11VO40) supported on mesoporous SBA-15. A series of HPA catalysts with HPA loadings varying from 10-50 wt% were prepared by impregnation method on SBA-15 support. The catalysts were characterized by X-ray diffraction, Raman spectroscopy, Fourier Transform infrared spectroscopy, temperature-programmed desorption of NH3, pyridine adsorbed FT-IR spectroscopy, scanning electron microscopy, pore size distribution and specific surface area measurements. The nature of acidic sites was examined by pyridine adsorbed FT-IR spectroscopy. XRD results suggest that the active phase containing HPA was highly dispersed at lower loadings on the support. FT-IR and Raman spectra results confirm that the presence of primary Keggin ion structure of HPA on the support and it was not affected during the preparation of catalysts. Pore size distribution results reveal that all the samples show unimodel pore size distribution with well depicted mesoporous structure. NH3-TPD results suggest that the acidity of catalysts increased with increase of HPA loading. The findings of acidity measurements by FT-IR spectra of pyridine adsorption reveals that the catalysts consist both the Brønsted and Lewis acidic sites and the amount of Brønsted acidic sites are increasing with HPA loading. SBA-15 supported vanadium substituted phosphomolybdic acid catalysts are found to be highly active during the dehydration reaction and exhibited 100% conversion of glycerol (10 wt% of glycerol) and the acrolein selectivity was appreciably changed with HPA active phase loading. The catalytic functionalities during glycerol dehydration are well correlated with surface acidity of the catalysts.

  6. Amino acid substitution converts WEREWOLF function from an activator to a repressor of Arabidopsis non-hair cell development.

    Tominaga-Wada, Rumi; Nukumizu, Yuka; Wada, Takuji

    2012-02-01

    Root hair cell or non-hair cell fate determination in Arabidopsis thaliana root epidermis is model system for plant cell development. Two types of MYB transcription factors, the R2R3-type MYB, WEREWOLF (WER), and an R3-type MYB, CAPRICE (CPC), are involved in this cell fate determination process. To study the molecular basis of this process, we analyzed the functional relationship of WER and CPC. WER-CPC chimeric constructs were made from WER where all or parts of the MYB R3 region were replaced with the corresponding regions from CPC R3, and the constructs were introduced into the cpc-2 mutant. Although, the WER gene did not rescue the cpc-2 mutant 'small number of root hairs' phenotype, the WER-CPC chimera with two amino acids substitution (WC6) completely rescued the cpc-2 mutant phenotype. Furthermore, the WER-CPC chimera with 37 amino acids substitution (WC5) excessively rescued the cpc-2 mutant and induced 2.5 times more root hairs than wild-type. Consistent with this phenotype, GL2 gene expression was strongly reduced in WC5 in a cpc-2 background. Our results suggest that swapping at least two amino acids is sufficient to convert WER to CPC function. Therefore, these key residues may have strongly contributed to the selection of these important functions over evolution.

  7. Theoretical Studies on Electronic Spectra and Second-order Nonlinear Optical Properties of Barbituric Acid Derivatives Substituted with Schiff Base

    SUN,Gang(孙刚); QIU,Yong-Qing(仇永清); SUN,Hai-Zhu(孙海珠); SU,Zhong-Min(苏忠民); FENG,Jing-Dong(冯静东); ZHU,Yu-Lan(朱玉兰)

    2004-01-01

    The structures of barbituric acid derivatives substituted with Schiff base were optimized using ab initio HF method at 6-31G basis set.Based on the optimized structures,the electronic spectra were obtained by INDO/CI method.The second-order nonlinear optical (NLO) coefficients βu were calculated according to the sum-over-states (SOS) formula.In addition,the effect of conjugation on electronic spectra and second-order NLO coefficients was investigated.The influence of exchange between C and N atoms as well as the substituted effect on the barbituric acid was discussed.It was indicated that the exchange between C and N atoms on Schiff base is important for enhancing the NLO coefficient of the whole molecule with donor and acceptor (D-A).Meanwhile significant changes in electron donation and acception were observed as substituents changes positions.Among the designed models,molecule 1b has maximal βμ value of 124.65 × 10-30 esu.About molecule 1b,barbituric acid is considered as an accepted electronic group and the position of N atom on Schiff base is close to it.

  8. Surgical technique: establishing a pre-clinical large animal model to test aortic valve leaflet substitute

    Knirsch, Walter; Cesarovic, Niko; Krüger, Bernard; Schmiady, Martin; Frauenfelder, Thomas; Frese, Laura; Dave, Hitendu; Hoerstrup, Simon Philipp; Hübler, Michael

    2016-01-01

    To overcome current limitations of valve substitutes and tissue substitutes the technology of tissue engineering (TE) continues to offer new perspectives in congenital cardiac surgery. We report our experiences and results implanting a decellularized TE patch in nine sheep in orthotropic position as aortic valve leaflet substitute. Establishing the animal model, feasibility, cardiopulmonary bypass issues and operative technique are highlighted. PMID:28149571

  9. Synthesis of novel N1-substituted bicyclic pyrazole amino acids and evaluation of their interaction with glutamate receptors

    Conti, Paola; Grazioso, Giovanni; di Ventimiglia, Samuele Joppolo

    2005-01-01

    N1-substituted bicyclic pyrazole amino acids (S)-9a-9c and (R)-9a-9c, which are conformationally constrained analogues of glutamic acid, were prepared via a strategy based on a 1,3-dipolar cycloaddition. The new amino acids were tested for activity at ionotropic and metabotropic glutamate receptors...

  10. Assessing the relative importance of the biophysical properties of amino acid substitutions associated with human genetic disease

    Terp, Bent N; Cooper, David N; Christensen, Inge T

    2002-01-01

    clinical observation likelihood (RCOL), can be regarded as a function of the structural/functional consequences of a mutation at the protein level. Following this paradigm, we modeled in silico all amino acid replacements that could potentially have arisen from an inherited single base pair substitution...... in five human genes encoding arylsulphatase A (ARSA), antithrombin III (SERPINC1), protein C (PROC), phenylalanine hydroxylase (PAH), and transthyretin (TTR). These proteins were chosen on the basis of 1) the availability of a crystallographic structure, and 2) a sufficiently large number of amino acid....... Nine parameters (including energy difference between wild-type and mutant structures, accessibility of the mutated residue, and distance from the binding/active site) exhibited statistically significant variability in their RCOL profiles, indicating that mutation-associated changes affected protein...

  11. Co-metabolic formation of substituted phenylacetic acids by styrene-degrading bacteria

    Michel Oelschlägel

    2015-06-01

    The styrene-degrading strains Rhodococcus opacus 1CP, Pseudomonas fluorescens ST, and the novel isolates Sphingopyxis sp. Kp5.2 and Gordonia sp. CWB2 were investigated with respect to their applicability to co-metabolically produce substituted phenylacetic acids. Isolates were found to differ significantly in substrate tolerance and biotransformation yields. Especially, P. fluorescens ST was identified as a promising candidate for the production of several phenylacetic acids. The biotransformation of 4-chlorostyrene with cells of strain ST was shown to be stable over a period of more than 200 days and yielded about 38 mmolproduct gcelldryweight−1 after nearly 350 days. Moreover, 4-chloro-α-methylstyrene was predominantly converted to the (S-enantiomer of the acid with 40% enantiomeric excess.

  12. Decarboxylation of substituted cinnamic acids by lactic acid bacteria isolated during malt whisky fermentation.

    van Beek, S; Priest, F G

    2000-12-01

    Seven strains of Lactobacillus isolated from malt whisky fermentations and representing Lactobacillus brevis, L. crispatus, L. fermentum, L. hilgardii, L. paracasei, L. pentosus, and L. plantarum contained genes for hydroxycinnamic acid (p-coumaric acid) decarboxylase. With the exception of L. hilgardii, these bacteria decarboxylated p-coumaric acid and/or ferulic acid, with the production of 4-vinylphenol and/or 4-vinylguaiacol, respectively, although the relative activities on the two substrates varied between strains. The addition of p-coumaric acid or ferulic acid to cultures of L. pentosus in MRS broth induced hydroxycinnamic acid decarboxylase mRNA within 5 min, and the gene was also induced by the indigenous components of malt wort. In a simulated distillery fermentation, a mixed culture of L. crispatus and L. pentosus in the presence of Saccharomyces cerevisiae decarboxylated added p-coumaric acid more rapidly than the yeast alone but had little activity on added ferulic acid. Moreover, we were able to demonstrate the induction of hydroxycinnamic acid decarboxylase mRNA under these conditions. However, in fermentations with no additional hydroxycinnamic acid, the bacteria lowered the final concentration of 4-vinylphenol in the fermented wort compared to the level seen in a pure-yeast fermentation. It seems likely that the combined activities of bacteria and yeast decarboxylate p-coumaric acid and then reduce 4-vinylphenol to 4-ethylphenol more effectively than either microorganism alone in pure cultures. Although we have shown that lactobacilli participate in the metabolism of phenolic compounds during malt whisky fermentations, the net result is a reduction in the concentrations of 4-vinylphenol and 4-vinylguaiacol prior to distillation.

  13. Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis.

    Mishra, Rajeev; Gara, Sudheer Kumar; Mishra, Shambhavi; Prakash, Balaji

    2005-05-01

    Ras superfamily GTP-binding proteins regulate important signaling events in the cell. Ras, which often serves as a prototype, efficiently hydrolyzes GTP in conjunction with its regulator GAP. A conserved glutamine plays a vital role in GTP hydrolysis in most GTP-binding proteins. Mutating this glutamine in Ras has oncogenic effects, since it disrupts GTP hydrolysis. The analysis presented here is of GTP-binding proteins that are a paradox to oncogenic Ras, since they have the catalytic glutamine (Glncat) substituted by a hydrophobic amino acid, yet can hydrolyze GTP efficiently. We term these proteins HAS-GTPases. Analysis of the amino acid sequences of HAS-GTPases reveals prominent presence of insertions around the GTP-binding pocket. Homology modeling studies suggest an interesting means to achieve catalysis despite the drastic hydrophobic substitution replacing the key Glncat of Ras-like GTPases. The substituted hydrophobic residue adopts a "retracted conformation," where it is positioned away from the GTP, as its role in catalysis would be unproductive. This conformation is further stabilized by interactions with hydrophobic residues in its vicinity. These interacting residues are strongly conserved and hydrophobic in all HAS-GTPases, and correspond to residues Asp92 and Tyr96 of Ras. An experimental support for the "retracted conformation" of Switch II arises from the crystal structures of Ylqf and hGBP1. This conformation allows us to hypothesize that, unlike in classical GTPases, catalytic residues could be supplied by regions other than the Switch II (i.e., either the insertions or a neighboring domain).

  14. Synthesis and anticancer evaluation of 2-phenyl thiaolidinone substituted 2-phenyl benzothiazole-6-carboxylic acid derivatives

    Padmavathi P. Prabhu

    2015-03-01

    Full Text Available A novel series of 2-(3-(4-oxo-2-substituted phenyl thiazolidin-3-ylphenylbenzo[d]thiazole-6-carboxylic acid derivatives PP1–PP8 were synthesized by various benzothiazole Schiff’s bases by reaction with thioglycollic acid. Their structures were established on the basis of IR, 1H-NMR, 13C-NMR, mass spectral data and elemental analysis. All the synthesized compounds were screened for their in vitro anticancer activity by 3-(4,5-dimethyl thiazole-2yl-2,5-diphenyltetrazoliumbromide (MTT assay on human cervical cancer cell line (HeLa cell lines. Among these compound PP2 exhibited most significant activity as compared with PP5, PP7 and PP8. However, the activity was less as compared to the standard drug Cisplatin.

  15. Fast enantioselective separation of clevidipine and a dihydropyridine substituted acid by SFC on Chiralpak AD.

    Gyllenhaal, O

    2001-01-01

    Conditions for the fast separation of the enantiomers of a dihydropyridine substituted acid on a 50 x 4.6 mm ID short Chiralpak AD column with 2-propanol modified carbon dioxide as the mobile phase are presented. A high throughout of samples can be accomplished through the continuous sample loading of the loop of the injector. If a continuous data collection was used 10 separations could be performed in about 5 min with a precision of 0.6% RSD for the area ratio (n = 10). The parent drug clevidipine can also be analyzed and its enantiomeric composition determined after alkaline hydrolysis into its acid, either through hydrolysis followed by extraction to dichloromethane or by direct analysis of the hydrolysis media. About 1 min is required for each run. Using 0.1 M of methanolic sodium hydroxide 2 min are sufficient for the hydrolysis, and, including weighing, only 5 min are required to analyze clevidipine.

  16. C-6 aryl substituted 4-quinolone-3-carboxylic acids as inhibitors of hepatitis C virus.

    Chen, Yue-Lei; Zacharias, Jeana; Vince, Robert; Geraghty, Robert J; Wang, Zhengqiang

    2012-08-01

    Quinolone-3-carboxylic acid represents a highly privileged chemotype in medicinal chemistry and has been extensively explored as antibiotics and antivirals targeting human immunodeficiency virus (HIV) integrase (IN). Herein we describe the synthesis and anti-hepatitis C virus (HCV) profile of a series of C-6 aryl substituted 4-quinlone-3-carboxylic acid analogues. Significant inhibition was observed with a few analogues at low micromolar range against HCV replicon in cell culture and a reduction in replicon RNA was confirmed through an RT-qPCR assay. Interestingly, evaluation of analogues as inhibitors of NS5B in a biochemical assay yielded only modest inhibitory activities, suggesting that a different mechanism of action could operate in cell culture.

  17. Synthesis, Characterization, and Antifungal Activity of Phenylpyrrole-Substituted Tetramic Acids Bearing Carbonates

    Wen-Qin Xu

    2016-03-01

    Full Text Available For the aim of discovering new fungicide, a series of phenylpyrrole-substituted tetramic acid derivatives bearing carbonates 6a–q were designed and synthesized via 4-(2,4-dioxopyrrolidin-3-ylidene-4-(phenylaminobutanoic acids 4a–k and the cyclized products 1′,3,4,5′-tetrahydro-[2,3′-bipyrrolylidene]-2′,4′,5(1H-triones 5a–k. The compounds were characterized using IR, 1H- and 13C-NMR spectroscopy, mass spectrometry (EI-MS, and elemental analysis. The structure of 6b was confirmed by X-ray diffraction crystallography. The title compounds 6a–q were bioassayed in vitro against the phytopathogenic fungi Fusarium graminearum, Botrytis cinerea and Rhizoctonia solani at a concentration of 100 μg/mL, respectively. Most compounds displayed good inhibitory activity.

  18. Synthesis and Characterization of Vanadium Substituted Dawson-Type Heteropoly Acid (Mo, As)

    ZHANG Jing; LI Juan; YU Li-qiong; WEI Xian-yin; LIU Li-ping; HUANG Ru-dan

    2006-01-01

    Five novel vanadium substituted series of Dawson-type heteropoly acid H7 [As2Mo17VO62 ]·10H2O (1), H8 [As2Mo16V2O62]·7H2O (2), H9 [As2Mo15V3O62 ]·8H2O (3), H8 [As2Mo14V4O62 H2]·7H2O (4), H9 [As2Mo13V5O62H2]·10H2O(5) were prepared respectively in aqueous solution. When magnetic stirring and pH meter monitoring, all reactants mixed and controled different pH, then the mixture was refluxed for 10 h, later extracted by aether when it cooled, finally, it could be recrystaled by 0.5 96 sulphuic acid solution, then yielded productions that we need. Compounds ( 1 ) - (5) were characterized by elemental analysis, thermogravimetic analysis (TGA), infrared spectroscopy (IR), ultraviolet and visible spectroscopy(UV-Vis), X-ray powder diffraction analysis, 51V nuclear magnetic resonance (51V NMR) structure analysis. The study indicates that these compounds possess Dawson structures. 51V NMR spectra reveals that V atom is polar-site substituted indeed.

  19. A1/A2-Diamino-Substituted Pillar[5]arene-Based Acid-Base-Responsive Host-Guest System.

    Hu, Wei-Bo; Hu, Wen-Jing; Zhao, Xiao-Li; Liu, Yahu A; Li, Jiu-Sheng; Jiang, Biao; Wen, Ke

    2016-05-06

    An acid-base-responsive supramolecular host-guest system based on a planarly chiral A1/A2-diamino-substituted pillar[5]arene (1)/imidazolium ion recognition motif was created. The pillar[4]arene[1]diaminobenzene 1 can bring an electron-deficient imidazolium cation into its cylindrically shaped cavity under neutral or basic conditions and release it under acidic conditions.

  20. Reactions of sulfur- and phosphorus-substituted fluoroalkylating silicon reagents with imines and enamines under acidic conditions.

    Kosobokov, Mikhail D; Dilman, Alexander D; Struchkova, Marina I; Belyakov, Pavel A; Hu, Jinbo

    2012-02-17

    Nucleophilic fluoroalkylation reactions of imines and enamines with α-phenylthio, α-phenylsulfonyl, and α-diethylphosphoryl substituted fluorinated silanes have been investigated. The reactions are promoted by hydrofluoric acid generated in situ from potassium hydrodifluoride and trifluoroacetic acid. Sulfur reagents worked well with both imines and enamines, whereas phosphorus reagent efficiently coupled only with enamines.

  1. Highly efficient coupling of beta-substituted aminoethane sulfonyl azides with thio acids, toward a new chemical ligation reaction.

    Merkx, Remco; Brouwer, Arwin J; Rijkers, Dirk T S; Liskamp, Rob M J

    2005-03-17

    [reaction: see text] A highly efficient coupling of protected beta-substituted aminoethane sulfonyl azides with thio acids is reported. In the case of peptide thio acids, this method encompasses a new chemoselective ligation method. Furthermore, the resulting alpha-amino acyl sulfonamides can be alkylated with suitable electrophiles to obtain densely functionalized sulfonamide scaffolds.

  2. Longer duration of viremia and unique amino acid substitutions in a hepatitis A virus strain [corrected] associated with Guillain-Barré syndrome (GBS).

    Joshi, Madhuri S; Cherian, Sarah S; Bhalla, Shilpa; Chitambar, Shobha D

    2010-05-01

    The molecular characteristics of hepatitis A virus (HAV) have been studied widely though there is a paucity of data on the correlation with virological and serological findings. In the present study, the whole genome of an Indian HAV strain associated with Guillain-Barré syndrome (GBS) was characterized vis-à-vis two other Indian HAV genotype IIIA strains, associated with a self-limiting disease. The percentage nucleotide divergence displayed by the Indian strains (CP-IND, PN-IND, and GBS-IND) varied from 3 to 6, whereas the percentage amino acid divergence varied from 0.1 to 0.7 as compared to the other HAV IIIA strains (n = 5) available in the GenBank. The GBS-IND strain showed an increased rate of nonsynonymous substitutions as well as a larger number of unique and heterologous amino acid substitutions compared to the HAV IIIA GenBank strains. These amino acid substitutions in the GBS-IND strain were detected in a nonstructural protein (2C-251F) and the B-cell epitope regions of structural proteins (VP1-29E, VP1-91S, VP3-50Y, and VP4-5S). In a comparative analysis of HAV strains, homology-based models of the capsid proteins indicated a localized alteration in the surface charge distribution on the VP1 protein of GBS-IND strain and involvement of its unique amino acid substitutions in the predicted antigenic determinants. Overall, the study suggests that the unique amino acid substitutions in the GBS-IND strain may have contributed to neutralization escape of the virus leading to a longer duration of viremia.

  3. Stearic acid: a possible substitute for trans fatty acids from industrial origin

    Tavella, Marcelo

    2011-06-01

    Full Text Available Trans isomers, contained in partially hydrogenated oils, which are used in the food industry, have been questioned and nowadays trends are heading towards reducing their consumption. The food industry is facing a dilemma, since in order to remove trans fatty acids, hydrogenated fats should be eliminated and replaced by fats rich in saturated fatty acids. Scientific research has shown that saturated fatty acids have negative effects on the lipid profile and its consumption is associated with a higher cardiovascular risk. Therefore it is recommended to avoid their consumption. Nevertheless, not all fatty acids behave in the same way, with stearic acid (18:0 the exception. Stearic acid has a low level of intestinal absorption and its intake does not negatively modify the lipid profile. For this reason, it is considered a “neutral” fatty acid with regard to cardiovascular health. B-100 apolipoprotein, whose levels determine plasma VLDL and LDL concentration (triglycerides and cholesterol carriers, respectively, is not modified by diets which provide up to 7% of the energy as stearic acid. Markers of cardiovascular risk, such as activation of platelet aggregation factors or C-reactive protein levels, are not modified by diets providing stearic acid, as occurs with other saturated fatty acids. The confirmation of the “neutral” effect of stearic acid represents a perspective for the development of fats with high contents of this fatty acid to replace hydrogenated fats containing trans isomers. The present review discusses these aspects.Los isómeros trans que contienen los aceites parcialmente hidrogenados de origen industrial, han sido cuestionados y la recomendación es reducir su consumo. La industria de alimentos se enfrenta a un dilema, ya que para disminuir los isómeros trans debe reducir los aceites parcialmente hidrogenados y reemplazarlos por grasas ricas en ácidos grasos saturados. La investigación ha demostrado que los

  4. Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met).

    Riffet, Vanessa; Frison, Gilles; Bouchoux, Guy

    2011-11-07

    Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra.

  5. SINGLE-PERIOD TWO-PRODUCT INVENTORY MODEL WITH SUBSTITUTION:SOLUTION AND PROPERTIES

    Lianqiao CAI; Jian CHEN; Houmin YAN

    2004-01-01

    In this paper, we study a single-period two-product inventory model with stochastic demands and downward substitution. The optimal order quantities are presented and some properties are provided. Comparing with newsboy model, we prove that both the profit and the fill rate can be improved by using the substitution policy.

  6. Computational Modeling of Degradation of Substituted Benzyltrimethyl Ammonium: Preprint

    Long, H.; Pivovar, B. S.

    2014-09-01

    The degradation of cations on the alkaline exchange membranes is the major challenge for alkaline membrane fuel cells. In this paper, we investigated the degradation barriers by density functional theory for substituted benzyltrimethyl ammonium (BTMA+) cations, which is one of the most commonly used cations for alkaline exchange membranes. We found that substituted cations with electron-releasing substituent groups at meta-position of the benzyl ring could result in improved degradation barriers. However, after investigating more than thirty substituted BTMA+ cations with ten different substituent groups, the largest improvement of degradation barriers is only 1.6 kcal/mol. This implies that the lifetime of alkaline membrane fuel cells could increase from a few months to a few years by using substituted BTMA+ cations, an encouraging but still limited improvement for real-world applications.

  7. Using video modeling with substitutable loops to teach varied play to children with autism.

    Dupere, Sally; MacDonald, Rebecca P F; Ahearn, William H

    2013-01-01

    Children with autism often engage in repetitive play with little variation in the actions performed or items used. This study examined the use of video modeling with scripted substitutable loops on children's pretend play with trained and untrained characters. Three young children with autism were shown a video model of scripted toy play that included a substitutable loop that allowed various characters to perform the same actions and vocalizations. Three characters were modeled with the substitutable loop during training sessions, and 3 additional characters were present in the video but never modeled. Following video modeling, all the participants incorporated untrained characters into their play, but the extent to which they did so varied.

  8. An amino acid substitution (L925V associated with resistance to pyrethroids in Varroa destructor.

    Joel González-Cabrera

    Full Text Available The Varroa mite, Varroa destructor, is an important pest of honeybees and has played a prominent role in the decline in bee colony numbers over recent years. Although pyrethroids such as tau-fluvalinate and flumethrin can be highly effective in removing the mites from hives, their intensive use has led to many reports of resistance. To investigate the mechanism of resistance in UK Varroa samples, the transmembrane domain regions of the V. destructor voltage-gated sodium channel (the main target site for pyrethroids were PCR amplified and sequenced from pyrethroid treated/untreated mites collected at several locations in Central/Southern England. A novel amino acid substitution, L925V, was identified that maps to a known hot spot for resistance within the domain IIS5 helix of the channel protein; a region that has also been proposed to form part of the pyrethroid binding site. Using a high throughput diagnostic assay capable of detecting the mutation in individual mites, the L925V substitution was found to correlate well with resistance, being present in all mites that had survived tau-fluvalinate treatment but in only 8 % of control, untreated samples. The potential for using this assay to detect and manage resistance in Varroa-infected hives is discussed.

  9. An amino acid substitution (L925V) associated with resistance to pyrethroids in Varroa destructor.

    González-Cabrera, Joel; Davies, T G Emyr; Field, Linda M; Kennedy, Peter J; Williamson, Martin S

    2013-01-01

    The Varroa mite, Varroa destructor, is an important pest of honeybees and has played a prominent role in the decline in bee colony numbers over recent years. Although pyrethroids such as tau-fluvalinate and flumethrin can be highly effective in removing the mites from hives, their intensive use has led to many reports of resistance. To investigate the mechanism of resistance in UK Varroa samples, the transmembrane domain regions of the V. destructor voltage-gated sodium channel (the main target site for pyrethroids) were PCR amplified and sequenced from pyrethroid treated/untreated mites collected at several locations in Central/Southern England. A novel amino acid substitution, L925V, was identified that maps to a known hot spot for resistance within the domain IIS5 helix of the channel protein; a region that has also been proposed to form part of the pyrethroid binding site. Using a high throughput diagnostic assay capable of detecting the mutation in individual mites, the L925V substitution was found to correlate well with resistance, being present in all mites that had survived tau-fluvalinate treatment but in only 8 % of control, untreated samples. The potential for using this assay to detect and manage resistance in Varroa-infected hives is discussed.

  10. High temperature dissolution of chromium substituted nickel ferrite in nitrilotriacetic acid medium

    Sathyaseelan, V. S.; Chandramohan, P.; Velmurugan, S.

    2016-12-01

    High temperature (HT) dissolution of chromium substituted nickel ferrite was carried out with relevance to the decontamination of nuclear reactors by way of chemical dissolution of contaminated corrosion product oxides present on stainless steel coolant circuit surfaces. Chromium substituted nickel ferrites of composition, NiFe(2-x)CrxO4 (x ≤ 1), was synthetically prepared and characterized. HT dissolution of these oxides was carried out in nitrilotriacetic acid medium at 160 °C. Dissolution was remarkably increased at 160 °C when compared to at 85 °C in a reducing decontamination formulation. Complete dissolution could be achieved for the oxides with chromium content 0 and 0.2. Increasing the chromium content brought about a marked reduction in the dissolution rate. About 40 fold decrease in rate of dissolution was observed when chromium was increased from 0 to 1. The rate of dissolution was not very significantly reduced in the presence of N2H4. Dissolution of oxide was found to be stoichiometric.

  11. Impact of the E540V amino acid substitution in GyrB of Mycobacterium tuberculosis on quinolone resistance.

    Kim, Hyun; Nakajima, Chie; Yokoyama, Kazumasa; Rahim, Zeaur; Kim, Youn Uck; Oguri, Hiroki; Suzuki, Yasuhiko

    2011-08-01

    Amino acid substitutions conferring resistance to quinolones in Mycobacterium tuberculosis have generally been found within the quinolone resistance-determining regions (QRDRs) in the A subunit of DNA gyrase (GyrA) rather than the B subunit of DNA gyrase (GyrB). To clarify the contribution of an amino acid substitution, E540V, in GyrB to quinolone resistance in M. tuberculosis, we expressed recombinant DNA gyrases in Escherichia coli and characterized them in vitro. Wild-type and GyrB-E540V DNA gyrases were reconstituted in vitro by mixing recombinant GyrA and GyrB. Correlation between the amino acid substitution and quinolone resistance was assessed by the ATP-dependent DNA supercoiling assay, quinolone-inhibited supercoiling assay, and DNA cleavage assay. The 50% inhibitory concentrations of eight quinolones against DNA gyrases bearing the E540V amino acid substitution in GyrB were 2.5- to 36-fold higher than those against the wild-type enzyme. Similarly, the 25% maximum DNA cleavage concentrations were 1.5- to 14-fold higher for the E540V gyrase than for the wild-type enzyme. We further demonstrated that the E540V amino acid substitution influenced the interaction between DNA gyrase and the substituent(s) at R-7, R-8, or both in quinolone structures. This is the first detailed study of the contribution of the E540V amino acid substitution in GyrB to quinolone resistance in M. tuberculosis.

  12. Radioimmunoassay for anileridine, meperidine, and other N-substituted phenylpiperidine carboxylic acid esters

    Van Vunakis, H.; Freeman, D.S.; Gjika, H.B.

    1975-10-01

    Antibodies that bind an /sup 125/I-tyramyl derivative of N-succinylanileridine have been produced in animals immunized with N-succinylanileridine-hemocyanin conjugate. Several congeners and metabolites have been tested as competitors of this antigen-antibody reaction. The concentrations (in picomoles) required for 50 percent inhibition have been found to be: anileridine (0.2), meperidine (3.5), piminodine (3.8), diphenoxylate (20.5), normeperidine (20.0), meperidine acid (45,000) and anileridine acid (3,400). Although ester hydrolysis results in changes in inhibiting capacities on the order of 10/sup 4/, major structural changes in the substituent on the nitrogen of the piperidine ring are not readily recognized by the antibody. This radioimmunoassay can be used to study a variety of N-substituted phenylpiperidine carboxylic acid esters by relating the results to the standard curve obtained for the drug under investigation. For all practical purposes, alphaprodine, morphine and methadone do not interfere with the assay.

  13. Enantioselective Ring-Opening Polymerization of rac-Lactide Dictated by Densely Substituted Amino Acids.

    Sanchez-Sanchez, Ana; Rivilla, Ivan; Agirre, Maddalen; Basterretxea, Andere; Etxeberria, Agustin; Veloso, Antonio; Sardon, Haritz; Mecerreyes, David; Cossío, Fernando P

    2017-03-22

    Organocatalysis is becoming an important tool in polymer science because of its versatility and specificity. To date a limited number of organic catalysts have demonstrated the ability to promote stereocontrolled polymerizations. In this work we report one of the first examples of chirality transfer from a catalyst to a polymer in the organocatalyzed ring-opening polymerization (ROP) of rac-lactide (rac-LA). We have polymerized rac-LA using the diastereomeric densely substituted amino acids (2S,3R,4S,5S)-1-methyl-4-nitro-3,5-diphenylpyrrolidine-2-carboxylic acid (endo-6) and (2S,3S,4R,5S)-1-methyl-4-nitro-3,5-diphenylpyrrolidine-2-carboxylic acid (exo-6), combined with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) as a cocatalyst. Both diastereoisomers not only showed the ability to synthesize enriched isotactic polylactide with a Pm higher than 0.90 at room temperature but also were able to preferentially promote the polymerization of one of the isomers (l or d) with respect to the other. Thus, exo-6 preferentially polymerized l-lactide, whereas endo-6 preferred d-lactide as the substrate. Density functional theory calculations were conducted to investigate the origins of this unique stereocontrol in the polymerization, providing mechanistic insight and explaining why the chirality of the catalyst is able to define the stereochemistry of the monomer insertion.

  14. Meso-ester and carboxylic acid substituted BODIPYs with far-red and near-infrared emission for bioimaging applications

    Ni, Yong

    2014-01-21

    A series of meso-ester-substituted BODIPY derivatives 1-6 are synthesized and characterized. In particular, dyes functionalized with oligo(ethylene glycol) ether styryl or naphthalene vinylene groups at the α positions of the BODIPY core (3-6) become partially soluble in water, and their absorptions and emissions are located in the far-red or near-infrared region. Three synthetic approaches are attempted to access the meso-carboxylic acid (COOH)-substituted BODIPYs 7 and 8 from the meso-ester-substituted BODIPYs. Two feasible synthetic routes are developed successfully, including one short route with only three steps. The meso-COOH-substituted BODIPY 7 is completely soluble in pure water, and its fluorescence maximum reaches around 650 nm with a fluorescence quantum yield of up to 15 %. Time-dependent density functional theory calculations are conducted to understand the structure-optical properties relationship, and it is revealed that the Stokes shift is dependent mainly on the geometric change from the ground state to the first excited singlet state. Furthermore, cell staining tests demonstrate that the meso-ester-substituted BODIPYs (1 and 3-6) and one of the meso-COOH-substituted BODIPYs (8) are very membrane-permeable. These features make these meso-ester- and meso-COOH-substituted BODIPY dyes attractive for bioimaging and biolabeling applications in living cells. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Enzymatic production of enantiopure amino acids from mono-substituted hydantoin substrates.

    Matcher, Gwynneth F; Dorrington, Rosemary A; Burton, Stephanie G

    2012-01-01

    Biocatalytic conversion of 5-substituted hydantoin derivatives is an efficient method for the production of unnatural enantiomerically pure amino acids. The enzymes required to carry out this hydrolysis occur in a wide variety of eubacterial species each of which exhibit variations in substrate selectivity, enantiospecificity, and catalytic efficiency. Screening of the natural environment for bacterial strains capable of utilizing hydantoin as a nutrient source (as opposed to rational protein design of known enzymes) is a cost-effective and valuable approach for isolating microbial species with novel hydantoin-hydrolysing enzyme systems. Once candidate microbial isolates have been identified, characterization and optimization of the activity of target enzyme systems can be achieved by subjecting the hydantoin-hydrolysing system to physicochemical manipulations aimed at the enzymes activity within the natural host cells, expressed in a heterologous host, or as purified enzymes. The latter two options require knowledge of the genes encoding for the hydantoin-hydrolysing enzymes. This chapter describes the methods that can be used in conducting such development of hydantoinase-based biocatalytic routes for production of target amino acids.

  16. Unusual fatty acid substitution in lipids and lipopolysaccharides of Helicobacter pylori.

    Geis, G; Leying, H; Suerbaum, S; Opferkuch, W

    1990-01-01

    Cellular fatty acids, phospholipid fatty acids, and lipopolysaccharide fatty acids of four strains of Helicobacter pylori were analyzed by gas-liquid chromatography. The presence of myristic acid, palmitic acid, stearic acid, oleic acid, linoleic acid, 19-carbon cyclopropane fatty acid, beta-hydroxypalmitic acid, and beta-hydroxystearic acid was confirmed. In phospholipids, myristic acid and 19-carbon cyclopropane fatty acid were the major fatty acids. Hydroxy fatty acids and unsaturated fatt...

  17. Structure-activity relationship of daptomycin analogues with substitution at (2S, 3R) 3-methyl glutamic acid position.

    Lin, Du'an; Lam, Hiu Yung; Han, Wenbo; Cotroneo, Nicole; Pandya, Bhaumik A; Li, Xuechen

    2017-02-01

    Daptomycin is a highly effective lipopeptide antibiotic against Gram-positive pathogens. The presence of (2S, 3R) 3-methyl glutamic acid (mGlu) in daptomycin has been found to be important to the antibacterial activity. However the role of (2S, 3R) mGlu is yet to be revealed. Herein, we reported the syntheses of three daptomycin analogues with (2S, 3R) mGlu substituted by (2S, 3R) methyl glutamine (mGln), dimethyl glutamic acid and (2S, 3R) ethyl glutamic acid (eGlu), respectively, and their antibacterial activities. The detailed synthesis of dimethyl glutamic acid was also reported.

  18. Synthesis of substituted gamma-lactams through petasis-type addition of boronic acids to N-acyliminium lons

    Wu, Peng; Clausen, Mads Hartvig; Nielsen, Thomas Eiland

    2014-01-01

    ic N -acyliminium ions. Under the optimized conditions, entail ing the use of HFIP as solvent, both electron-rich and electron -deficient boronic acids were successfully added to a ran ge of cyclic N -acyliminium ions, thereby obtaining a collection of phar maceutically relevant substituted g...

  19. Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function

    Xi, T; Jones, I M; Mohrenweiser, H W

    2003-11-03

    Over 520 different amino acid substitution variants have been previously identified in the systematic screening of 91 human DNA repair genes for sequence variation. Two algorithms were employed to predict the impact of these amino acid substitutions on protein activity. Sorting Intolerant From Tolerant (SIFT) classified 226 of 508 variants (44%) as ''Intolerant''. Polymorphism Phenotyping (PolyPhen) classed 165 of 489 amino acid substitutions (34%) as ''Probably or Possibly Damaging''. Another 9-15% of the variants were classed as ''Potentially Intolerant or Damaging''. The results from the two algorithms are highly associated, with concordance in predicted impact observed for {approx}62% of the variants. Twenty one to thirty one percent of the variant proteins are predicted to exhibit reduced activity by both algorithms. These variants occur at slightly lower individual allele frequency than do the variants classified as ''Tolerant'' or ''Benign''. Both algorithms correctly predicted the impact of 26 functionally characterized amino acid substitutions in the APE1 protein on biochemical activity, with one exception. It is concluded that a substantial fraction of the missense variants observed in the general human population are functionally relevant. These variants are expected to be the molecular genetic and biochemical basis for the associations of reduced DNA repair capacity phenotypes with elevated cancer risk.

  20. Molecular dynamics investigations on the effect of D amino acid substitution in a triple-helix structure and the stability of collagen.

    Punitha, V; Raman, S Sundar; Parthasarathi, R; Subramanian, V; Rao, J Raghava; Nair, Balachandran Unni; Ramasami, T

    2009-07-02

    Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.

  1. Whole-cell biocatalytic production of variously substituted β-aryl- and β-heteroaryl-β-amino acids.

    Ratnayake, Nishanka Dilini; Theisen, Chelsea; Walter, Tyler; Walker, Kevin D

    2016-01-10

    Biologically-active β-peptides and pharmaceuticals that contain key β-amino acids are emerging as target therapeutics; thus, synthetic strategies to make substituted, enantiopure β-amino acids are increasing. Here, we use whole-cell Escherichia coli (OD600 ∼ 35) engineered to express a Pantoea agglomerans phenylalanine aminomutase (PaPAM) biocatalyst. In either 5 mL, 100mL, or 1L of M9 minimal medium containing α-phenylalanine (20mM), the cells produced ∼ 1.4 mg mL(-1) of β-phenylalanine in each volume. Representative pilot-scale 5-mL cultures, fermentation reactions converted 18 variously substituted α-arylalanines to their (S)-β-aryl-β-amino acids in vivo and were not toxic to cells at mid- to late-stage growth. The β-aryl-β-amino acids made ranged from 0.043 mg (p-nitro-β-phenylalanine, 4% converted yield) to 1.2mg (m-bromo-β-phenylalanine, 96% converted yield) over 6h in 5 mL. The substituted β-amino acids made herein can be used in redox and Stille-coupling reactions to make synthetic building blocks, or as bioisosteres in drug design.

  2. Selective oxidation of glycerol to formic acid in highly concentrated aqueous solutions with molecular oxygen using V-substituted phosphomolybdic acids

    Zhang, Jizhe

    2014-01-01

    Formic acid is an important commodity chemical as well as a promising medium for hydrogen storage and hydrogen production. In this paper, we report that formic acid can be produced through selective oxidation of glycerol, a low-cost by-product of biodiesel, by using vanadium-substituted phosphomolybdic acids as catalysts and molecular oxygen as the oxidant. Significantly, this catalytic system allows for high-concentration conversions and thus leads to exceptional efficiency. Specifically, 3.64 g of formic acid was produced from 10 g of glycerol/water (50/50 in weight) solution. © 2014 the Partner Organisations.

  3. High-Temperature Decomposition of Brønsted Acid Sites in Gallium-Substituted Zeolites

    K Al-majnouni; N Hould; W Lonergan; D Vlachos; R Lobo

    2011-12-31

    The dehydroxylation of Broensted acid sites (BAS) in Ga-substituted zeolites was investigated at temperatures up to 850 C using X-ray absorption spectroscopy (XAS), Fourier transform infrared spectroscopy (FTIR), and mass spectrometry-temperature programmed desorption (MS-TPD). X-ray absorption near-edge spectroscopy (XANES) revealed that the majority of gallium has tetrahedral coordination even after complete dehydroxylation. The interatomic gallium-oxygen distance and gallium coordination number determined by extended X-ray absorption fine structure (EXAFS) are consistent with gallium in tetrahedral coordination at low T (< 550 C). Upon heating Ga-Beta and Ga-ZSM5 to 850 C, analysis of the EXAFS showed that 70 and 80% of the gallium was still in tetrahedral coordination. The remainder of the gallium was found to be in octahedral coordination. No trigonal Ga atoms were observed. FTIR measurements carried out at similar temperatures show that the intensity of the OH vibration due to BAS has been eliminated. MS-TPD revealed that hydrogen in addition to water evolved from the samples during dehydroxylation. This shows that dehydrogenation in addition to dehydration is a mechanism that contributes to BAS decomposition. Dehydrogenation was further confirmed by exposing the sample to hydrogen to regenerate some of the BAS as monitored by FTIR and MS-TPD.

  4. Synthesis of Substituted Thioureas and Their Sulfur Heterocyclic Systems of p-Amino Salicylic Acid as Antimycobacterial Agents

    Mohammed Saleh I. T. Makki; Abdel-Rahman, Reda M.; Faidallah, Hassan M.; Khalid Ali Khan

    2013-01-01

    A series of new N,N′-substituted thioureas (2, 6, and 8) and their sulfur heterocycles as thiobarbituric acids (3, 4, and 7), 2-thioxothiazoliodin-4-one (10), thiazolidin-4-one (11), 1,2,4-triazol-5-thione (14), and 1,3,4-thiadiazole (15) of p-Amino salicylic acid (PAS) have been synthesized from treatment with dithiocarbazinate (1, 5 and 12) followed by heterocyclization with dimethyl malonate, chloroacetic acid, and/or trifluoroacetic anhydride. The structures of the newly synthesized compo...

  5. Acid rain: Mesoscale model

    Hsu, H. M.

    1980-01-01

    A mesoscale numerical model of the Florida peninsula was formulated and applied to a dry, neutral atmosphere. The prospective use of the STAR-100 computer for the submesoscale model is discussed. The numerical model presented is tested under synoptically undisturbed conditions. Two cases, differing only in the direction of the prevailing geostrophic wind, are examined: a prevailing southwest wind and a prevailing southeast wind, both 6 m/sec at all levels initially.

  6. Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model

    Sharma, Ity; Kaminski, George A.

    2012-01-01

    We have computed pKa values for eleven substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We ha...

  7. Acid rain: Microphysical model

    Dingle, A. N.

    1980-01-01

    A microphysical model was used to simulate the case of a ground cloud without dilution by entrainment and without precipitation. The numerical integration techniques of the model are presented. The droplet size spectra versus time and the droplet molalities for each value of time are discussed.

  8. A new approach for estimating the efficiencies of the nucleotide substitution models.

    Som, Anup

    2007-04-01

    In this article, a new approach is presented for estimating the efficiencies of the nucleotide substitution models in a four-taxon case and then this approach is used to estimate the relative efficiencies of six substitution models under a wide variety of conditions. In this approach, efficiencies of the models are estimated by using a simple probability distribution theory. To assess the accuracy of the new approach, efficiencies of the models are also estimated by using the direct estimation method. Simulation results from the direct estimation method confirmed that the new approach is highly accurate. The success of the new approach opens a unique opportunity to develop analytical methods for estimating the relative efficiencies of the substitution models in a straightforward way.

  9. Synthesis of New Fluorine Substituted Heterocyclic Nitrogen Systems Derived from p-Aminosalicylic Acid as Antimycobacterial Agents

    Mohammed Saleh I. T. Makki

    2013-01-01

    Full Text Available Some new fluorine substituted heterocyclic nitrogen systems 2–17 have been synthesized from ring closure reactions of substituted p-amino salicylic acids (PAS. The Schiffs base of PAS was cyclized with chloroacetyl chloride and mercaptoacetic acid to give azetidinone 2, thiazolidinone 3, and spiro-fluoroindolothiazoline-dione 10. However, PAS when reacted directly with 4-fluorobenzoyl chloride and 5-oxazolinone yielded derivatives 4, 5, and 7. Aminomethylation of PAS using formaldehyde and piperidine or piperazine formed N-alkyl and N,N′-dialkyl derivatives (11 and 12 respectively upon fluorinated benzoylation gave compounds 13 and 14. Similarly, treatment of PAS with thiosemicarbazide 15 and subsequent cyclization with diethyl oxalate yielded the fluorinated heterocycle 17. The structures of the fluorinated heterocyclic systems have been established on the basis of elemental analysis, 1H NMR, 13C NMR, and MS spectral data. Some of the targets exhibited a high inhibition towards Mycobacterium strain with favorable log P values.

  10. Stereoselective Michael Addition of Glycine Anions to Chiral Fischer Alkenylcarbene Complexes. Asymmetric Synthesis of beta-Substituted Glutamic Acids.

    Ezquerra, Jesús; Pedregal, Concepción; Merino, Isabel; Flórez, Josefa; Barluenga, José; García-Granda, Santiago; Llorca, María-Amparo

    1999-09-03

    The reaction of lithium enolates of achiral N-protected glycine esters with chiral alkoxyalkenylcarbene complexes of chromium provided the corresponding Michael adducts with either high anti or syn selectivity depending on the nature of the nitrogen protecting group, and high diastereofacial selectivity when carbene complexes containing the (-)-8-phenylmenthyloxy group were employed. Subsequent oxidation of the metal-carbene moiety followed by deprotection of the amine group and hydrolysis of both carboxylic esters afforded enantiomerically enriched 3-substituted glutamic acids of natural as well as unnatural stereochemistry. Alternatively, when the deprotection step was performed previously to the oxidation, cyclic aminocarbene complexes were formed, which finally led to optically active 3-substituted pyroglutamic acids.

  11. Growth and nitrogen metabolism of sea bass fed graded levels of nucleic acid nitrogen from yeast or RNA extract as partial substitute for protein nitrogen from fish meal

    S. Kaushik

    2010-01-01

    Full Text Available Some studies carried out in mammalian models have shown de novo synthesis and salvage of nucleotides to be a costly metabolic process and a dietary supplementation with nucleic acids (NA or nucleotides has been suggested to result in a protein sparing action (Sanderson and He, 1994. On the other hand, high levels of dietary NA could have toxic effects and lead to disturbance in protein, lipid and carbohydrate metabolism in monogastric animals lacking uricase activity, an enzyme involved in NA degradation (Clifford and Story, 1976. So far, there is no clear indication of such effects in fish fed nucleic acid-enriched diets (Tacon and Cooke, 1980; Rumsey et al., 1992; Fournier et al., 2002. The aim of this experiment was to investigate growth response and N metabolism in juvenile sea bass (D. labrax fed diets supplying graded levels of nucleic acid N from dry brewer's yeast or RNA extract as partial substitutes for protein nitrogen provided by fish meal.

  12. Imidase catalyzing desymmetric imide hydrolysis forming optically active 3-substituted glutaric acid monoamides for the synthesis of gamma-aminobutyric acid (GABA) analogs.

    Nojiri, Masutoshi; Hibi, Makoto; Shizawa, Hiroaki; Horinouchi, Nobuyuki; Yasohara, Yoshihiko; Takahashi, Satomi; Ogawa, Jun

    2015-12-01

    The recent use of optically active 3-substituted gamma-aminobutyric acid (GABA) analogs in human therapeutics has identified a need for an efficient, stereoselective method of their synthesis. Here, bacterial strains were screened for enzymes capable of stereospecific hydrolysis of 3-substituted glutarimides to generate (R)-3-substituted glutaric acid monoamides. The bacteria Alcaligenes faecalis NBRC13111 and Burkholderia phytofirmans DSM17436 were discovered to hydrolyze 3-(4-chlorophenyl) glutarimide (CGI) to (R)-3-(4-chlorophenyl) glutaric acid monoamide (CGM) with 98.1% enantiomeric excess (e.e.) and 97.5% e.e., respectively. B. phytofirmans DSM17436 could also hydrolyze 3-isobutyl glutarimide (IBI) to produce (R)-3-isobutyl glutaric acid monoamide (IBM) with 94.9% e.e. BpIH, an imidase, was purified from B. phytofirmans DSM17436 and found to generate (R)-CGM from CGI with specific activity of 0.95 U/mg. The amino acid sequence of BpIH had a 75% sequence identity to that of allantoinase from A. faecalis NBRC13111 (AfIH). The purified recombinant BpIH and AfIH catalyzed (R)-selective hydrolysis of CGI and IBI. In addition, a preliminary investigation of the enzymatic properties of BpIH and AfIH revealed that both enzymes were stable in the range of pH 6-10, with an optimal pH of 9.0, stable at temperatures below 40 °C, and were not metalloproteins. These results indicate that the use of this class of hydrolase to generate optically active 3-substituted glutaric acid monoamide could simplify the production of specific chiral GABA analogs for drug therapeutics.

  13. Effect of specific amino acid substitutions in the putative fusion peptide of structural glycoprotein E2 on Classical Swine Fever Virus replication

    Fernández-Sainz, I.J. [Plum Island Animal Disease Center, ARS, USDA (United States); Largo, E. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Gladue, D.P.; Fletcher, P. [Plum Island Animal Disease Center, ARS, USDA (United States); O’Donnell, V. [Plum Island Animal Disease Center, ARS, USDA (United States); Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Holinka, L.G. [Plum Island Animal Disease Center, ARS, USDA (United States); Carey, L.B. [Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), E-08003 Barcelona (Spain); Lu, X. [Plum Island Animal Disease Center, DHS, Greenport, NY 11944 (United States); Nieva, J.L. [Biophysics Unit (CSIC-UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao (Spain); Borca, M.V., E-mail: manuel.borca@ars.usda.gov [Plum Island Animal Disease Center, ARS, USDA (United States)

    2014-05-15

    E2, along with E{sup rns} and E1, is an envelope glycoprotein of Classical Swine Fever Virus (CSFV). E2 is involved in several virus functions: cell attachment, host range susceptibility and virulence in natural hosts. Here we evaluate the role of a specific E2 region, {sup 818}CPIGWTGVIEC{sup 828}, containing a putative fusion peptide (FP) sequence. Reverse genetics utilizing a full-length infectious clone of the highly virulent CSFV strain Brescia (BICv) was used to evaluate how individual amino acid substitutions within this region of E2 may affect replication of BICv. A synthetic peptide representing the complete E2 FP amino acid sequence adopted a β-type extended conformation in membrane mimetics, penetrated into model membranes, and perturbed lipid bilayer integrity in vitro. Similar peptides harboring amino acid substitutions adopted comparable conformations but exhibited different membrane activities. Therefore, a preliminary characterization of the putative FP {sup 818}CPIGWTGVIEC{sup 828} indicates a membrane fusion activity and a critical role in virus replication. - Highlights: • A putative fusion peptide (FP) region in CSFV E2 protein was shown to be critical for virus growth. • Synthetic FPs were shown to efficiently penetrate into lipid membranes using an in vitro model. • Individual residues in the FP affecting virus replication were identified by reverse genetics. • The same FP residues are also responsible for mediating membrane fusion.

  14. Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity.

    Nengyi Zhang

    Full Text Available BACKGROUND: Central carbon metabolism (CCM is a fundamental component of life. The participating genes and enzymes are thought to be structurally and functionally conserved across and within species. Association mapping utilizes a rich history of mutation and recombination to achieve high resolution mapping. Therefore, applying association mapping in maize (Zea mays ssp. mays, the most diverse model crop species, to study the genetics of CCM is a particularly attractive system. METHODOLOGY/PRINCIPAL FINDINGS: We used a maize diversity panel to test the CCM functional conservation. We found heritable variation in enzyme activity for every enzyme tested. One of these enzymes was the NAD-dependent isocitrate dehydrogenase (IDH, E.C. 1.1.1.41, in which we identified a novel amino-acid substitution in a phylogenetically conserved site. Using candidate gene association mapping, we identified that this non-synonymous polymorphism was associated with IDH activity variation. The proposed mechanism for the IDH activity variation includes additional components regulating protein level. With the comparison of sequences from maize and teosinte (Zea mays ssp. Parviglumis, the maize wild ancestor, we found that some CCM genes had also been targeted for selection during maize domestication. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate the efficacy of association mapping for dissecting natural variation in primary metabolic pathways. The considerable genetic diversity observed in maize CCM genes underlies heritable phenotypic variation in enzyme activities and can be useful to identify putative functional sites.

  15. Mass Spectrometry Analysis Coupled with de novo Sequencing Reveals Amino Acid Substitutions in Nucleocapsid Protein from Influenza A Virus

    Zijian Li

    2014-02-01

    Full Text Available Amino acid substitutions in influenza A virus are the main reasons for both antigenic shift and virulence change, which result from non-synonymous mutations in the viral genome. Nucleocapsid protein (NP, one of the major structural proteins of influenza virus, is responsible for regulation of viral RNA synthesis and replication. In this report we used LC-MS/MS to analyze tryptic digestion of nucleocapsid protein of influenza virus (A/Puerto Rico/8/1934 H1N1, which was isolated and purified by SDS poly-acrylamide gel electrophoresis. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. The obtained results provided experimental evidence that amino acid substitutions resulted from non-synonymous gene mutations could be directly characterized by mass spectrometry in proteins of RNA viruses such as influenza A virus.

  16. Nucleophilic substitution reactions of alcohols with use of montmorillonite catalysts as solid Brønsted acids.

    Motokura, Ken; Nakagiri, Nobuaki; Mizugaki, Tomoo; Ebitani, Kohki; Kaneda, Kiyotomi

    2007-08-03

    We have developed an environmentally benign synthetic approach to nucleophilic substitution reactions of alcohols that minimizes or eliminates the formation of byproducts, resulting in a highly atom-efficient chemical process. Proton- and metal-exchanged montmorillonites (H- and Mn+-mont) were prepared easily by treating Na+-mont with an aqueous solution of hydrogen chloride or metal salt, respectively. The H-mont possessed outstanding catalytic activity for nucleophilic substitution reactions of a variety of alcohols with anilines, because the unique acidity of the H-mont catalyst effectively prevents the neutralization by the basic anilines. In addition, amides, indoles, 1,3-dicarbonyl compounds, and allylsilane act as nucleophiles for the H-mont-catalyzed substitutions of alcohols, which allowed efficient formation of various C-N and C-C bonds. The solid H-mont was reusable without any appreciable loss in its catalytic activity and selectivity. Especially, an Al3+-mont showed high catalytic activity for the alpha-benzylation of 1,3-dicarbonyl compounds with primary alcohols due to cooperative catalysis between a protonic acid site and a Lewis acidic Al3+ species in its interlayer spaces.

  17. Modulation of anti-endotoxin property of Temporin L by minor amino acid substitution in identified phenylalanine zipper sequence.

    Srivastava, Saurabh; Kumar, Amit; Tripathi, Amit Kumar; Tandon, Anshika; Ghosh, Jimut Kanti

    2016-11-01

    A 13-residue frog antimicrobial peptide Temporin L (TempL) possesses versatile antimicrobial activities and is considered a lead molecule for the development of new antimicrobial agents. To find out the amino acid sequences that influence the anti-microbial property of TempL, a phenylalanine zipper-like sequence was identified in it which was not reported earlier. Several alanine-substituted analogs and a scrambled peptide having the same composition of TempL were designed for evaluating the role of this motif. To investigate whether leucine residues instead of phenylalanine residues at 'a' and/or 'd' position(s) of the heptad repeat sequence could alter its antimicrobial property, several TempL analogs were synthesized after replacing these phenylalanine residues with leucine residues. Replacing phenylalanine residues with alanine residues in the phenylalanine zipper sequence significantly compromised the anti-endotoxin property of TempL. This is evident from the higher production of tumor necrosis factor-α and interleukin-6 in lipopolysaccharide (LPS)-stimulated rat bone-marrow-derived macrophage cells in the presence of its alanine-substituted analogs than TempL itself. However, replacement of these phenylalanine residues with leucine residues significantly augmented anti-endotoxin property of TempL. A single alanine-substituted TempL analog (F8A-TempL) showed significantly reduced cytotoxicity but retained the antibacterial activity of TempL, while the two single leucine-substituted analogs (F5L-TempL and F8L-TempL), although exhibiting lower cytotoxicity, were able to retain the antibacterial activity of the parent peptide. The results demonstrate how minor amino acid substitutions in the identified phenylalanine zipper sequence in TempL could yield analogs with better antibacterial and/or anti-endotoxin properties with their plausible mechanism of action.

  18. Bone defect animal models for testing efficacy of bone substitute biomaterials

    Ye Li

    2015-07-01

    Full Text Available Large bone defects are serious complications that are most commonly caused by extensive trauma, tumour, infection, or congenital musculoskeletal disorders. If nonunion occurs, implantation for repairing bone defects with biomaterials developed as a defect filler, which can promote bone regeneration, is essential. In order to evaluate biomaterials to be developed as bone substitutes for bone defect repair, it is essential to establish clinically relevant in vitro and in vivo testing models for investigating their biocompatibility, mechanical properties, degradation, and interactional with culture medium or host tissues. The results of the in vitro experiment contribute significantly to the evaluation of direct cell response to the substitute biomaterial, and the in vivo tests constitute a step midway between in vitro tests and human clinical trials. Therefore, it is essential to develop or adopt a suitable in vivo bone defect animal model for testing bone substitutes for defect repair. This review aimed at introducing and discussing the most available and commonly used bone defect animal models for testing specific substitute biomaterials. Additionally, we reviewed surgical protocols for establishing relevant preclinical bone defect models with various animal species and the evaluation methodologies of the bone regeneration process after the implantation of bone substitute biomaterials. This review provides an important reference for preclinical studies in translational orthopaedics.

  19. Using Video Modeling with Substitutable Loops to Teach Varied Play to Children with Autism

    Dupere, Sally; MacDonald, Rebecca P. F.; Ahearn, William H.

    2013-01-01

    Children with autism often engage in repetitive play with little variation in the actions performed or items used. This study examined the use of video modeling with scripted substitutable loops on children's pretend play with trained and untrained characters. Three young children with autism were shown a video model of scripted toy play that…

  20. Effects of bis homoallylic and homoallylic hydroxyl substitution on the olefinic 13C resonance shifts in fatty acid methyl esters.

    Pfeffer, P E; Sonnet, P E; Schwartz, D P; Osman, S F; Weisleder, D

    1992-04-01

    Substitution of a hydroxyl group at the bis homoallylic position (OH group located three carbons away from the olefinic carbon) in C18 unsaturated fatty acid esters (FAE) induces a 0.73 +/- 0.05 ppm upfield and a 0.73 +/- 0.06 ppm downfield shift on the delta and epsilon olefinic 13C resonances relative to the unsubstituted FAE, respectively. If the hydroxyl group is located on the carboxyl side of the double bond of the bis homoallylic hydroxy fatty acid esters (BHAHFA), the olefinic resonances are uniformly shifted apart by [formula: see text] where delta delta dbu represents the absolute value of the double bond resonance separation in the unsubstituted FAE and 1.46 ppm is the sum of the absolute values of the delta and epsilon shift parameters. With hydroxyl substitution on the terminal methyl side of the double bond, the olefinic shift separation is equal to [formula: see text] In homoallylic (OH group located two carbons away from the olefinic carbon) substituted FAE the gamma and delta induced hydroxyl shifts for the cis double bond resonances are +3.08 and -4.63 ppm, respectively while the trans double bond parameters are +4.06 and -4.18 ppm, respectively. The double bond resonance separation in homoallylic hydroxy fatty acid esters (HAHFA) can be calculated from the formula [formula: see text] for cis and [formula: see text] for the trans case when the OH substitution is on the carboxyl side of the double bond. Conversely, when the OH resides on the terminal methyl side, the double bond shift separations for cis and trans isomers are [formula: see text] and [formula: see text] respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

  1. Design and Synthesis of p/m-[p-(un)Substituted Phenylsulfonamido]phenyl β-Diketo Acids and Quinoxalone Derivatives

    ZENG,Cheng-Chu; LI,Xue-Mei; YAN,Hong; ZHONG,Ru-Gang

    2007-01-01

    Diketo acid derivatives are potent and selective HIV-1 integrase inhibitors. To investigate the detailed synthesis of those derivatives, a series of p/m-[p-(un)substituted phenylsulfonamido]phenyl β-diketo acid derivatives have been designed and synthesized. The quinoxalone derivatives as the potential bioisosteres of the biologically labile β-diketoacid pharmacophores have also been synthesized from reactions of the corresponding diketo acids with o-phenylenediamine. The structures of all diketo acid (ester) and quinoxalone derivatives were confirmed by 1H NMR, 13C NMR, IR, HRMS and/or MS (ESI). X-ray crystallographic analysis of 11b demonstrates a similar arrangement of the side chain of quinoxalone derivatives with the parent diketoacids due to the intramolecular hydrogen bond (O…H-N) and the sp2 hybridization configuration of the two nitrogen atoms of the quinoxalone ring.

  2. Electro-membrane reactor for separation and in situ ion substitution of glutamic acid from its sodium salt

    Kumar, Mahendra; Tripathi, Bijay P. [Electro-Membrane Processes Division, Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research (CSIR), G. B. Marg, Bhavnagar 364002, Gujarat (India); Shahi, Vinod K. [Electro-Membrane Processes Division, Central Salt and Marine Chemicals Research Institute, Council of Scientific and Industrial Research (CSIR), G. B. Marg, Bhavnagar 364002, Gujarat (India)], E-mail: vkshahi@csmcri.org

    2009-08-30

    An electro-membrane reactor with four compartments (EMR-4) (anolyte, catholyte and comp. 1 and 2) based on in-house-prepared cation- and anion-exchange membrane (CEM and AEM, respectively) was developed to achieve separation and recovery of glutamic acid (GAH) from its sodium salt by in situ ion substitution and acidification. The physicochemical and electrochemical properties of CEM and AEM were characterized and its suitability was assessed in operating environment. The separation of GA{sup -} from the mixture of nonionic organic compounds and further ion substitution was achieved by EMR-4. But the higher energy consumption (5.75 kWh/kg of GAH produced), low current efficiency (50.5%) and recovery of GAH (57.2%) in this process were main obstacles for the industrial exploration of the process. Latter, electro-membrane reactor with three compartments (EMR-3) (anolyte, catholyte and central compartment) was developed based on CEMs for only in situ ion substitution of GANa to achieve GAH, in which GA{sup -} was not allowed for electro-migration from its feed compartment. CE and recovery of GAH were close to 73% and 96% that indicate the suitability of the EMR-3 process for industrial application over the EMR-4. It was concluded that EMR-3 was efficient as compared to EMR-4 for separation and recovery of GAH from fermentation broth by in situ ion substitution in eco-friendly manner.

  3. A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA.

    Shen, Li; Gao, Ge; Zhang, Ying; Zhang, He; Ye, Zhiqiang; Huang, Shichao; Huang, Jinyan; Kang, Jiuhong

    2010-10-01

    Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuring DNA methylation activity of Dnmt3a and Dnmt3b homologues from five species, we found that mammalian Dnmt3b possessed significantly higher methylation activity on chromatin DNA than Dnmt3a and non-mammalian Dnmt3b. Sequence comparison and mutagenesis experiments identified a single amino acid substitution (I662N) in mammalian Dnmt3b as being crucial for its high chromatin DNA methylation activity. Further mechanistic studies demonstrated this substitution markedly enhanced the binding of Dnmt3b to nucleosomes and hence increased the chromatin DNA methylation activity. Moreover, this substitution was crucial for Dnmt3b to efficiently methylate repetitive sequences, which increased dramatically in mammalian genomes. Consistent with our observation that Dnmt3b evolved more rapidly than Dnmt3a during the emergence of mammals, these results demonstrated that the I662N substitution in mammalian Dnmt3b conferred enhanced chromatin DNA methylation activity and contributed to functional adaptation in the epigenetic system.

  4. Effect of α-Methyl versus α-Hydrogen Substitution on Brain Availability and Tumor Imaging Properties of Heptanoic [F-18]Fluoroalkyl Amino Acids for Positron Emission Tomography (PET).

    Bouhlel, Ahlem; Alyami, Wadha; Li, Aixiao; Yuan, Liya; Rich, Keith; McConathy, Jonathan

    2016-04-14

    Two [(18)F]fluoroalkyl substituted amino acids differing only by the presence or absence of a methyl group on the α-carbon, (S)-2-amino-7-[(18)F]fluoro-2-methylheptanoic acid ((S)-[(18)F]FAMHep, (S)-[(18)F]14) and (S)-2-amino-7-[(18)F]fluoroheptanoic acid ((S)-[(18)F]FAHep, (S)-[(18)F]15), were developed for brain tumor imaging and compared to the well-established system L amino acid tracer, O-(2-[(18)F]fluoroethyl)-l-tyrosine ([(18)F]FET), in the delayed brain tumor (DBT) mouse model of high-grade glioma. Cell uptake, biodistribution, and PET/CT imaging studies showed differences in amino acid transport of these tracer by DBT cells. Recognition of (S)-[(18)F]15 but not (S)-[(18)F]14 by system L amino acid transporters led to approximately 8-10-fold higher uptake of the α-hydrogen substituted analogue (S)-[(18)F]15 in normal brain. (S)-[(18)F]15 had imaging properties similar to those of (S)-[(18)F]FET in the DBT tumor model while (S)-[(18)F]14 afforded higher tumor to brain ratios due to much lower uptake by normal brain. These results have important implications for the future development of α-alkyl and α,α-dialkyl substituted amino acids for brain tumor imaging.

  5. Synthesis and structure--activity relationships of substituted cinnamic acids and amide analogues: a new class of herbicides.

    Vishnoi, Shipra; Agrawal, Vikash; Kasana, Virendra K

    2009-04-22

    In the present investigation, substituted cinnamic acids (3-hydroxy, 4-hydroxy, 2-nitro, 3-nitro, 4-nitro, 3-chloro, and 4-methoxy) and their amide analogues with four different types of substituted anilines have been synthesized. The synthesized compounds have been screened for their germination inhibition activity on radish (Raphanus sativus L. var. Japanese White) seeds at 50, 100, and 200 ppm concentrations, and the activity was compared with standard herbicide, metribuzin formulation (sencor). Significant activity was exhibited by all of the compounds. It was observed that with the increase in concentration of the test solution, the activity also increased. All of the compounds showed more than 70% inhibition at 100 ppm concentration except 4-hydroxy cinnamanilide. The compound, 2-chloro (4'-hydroxy) cinnamanilide was the best among the tested compounds, and it was found to be at par with the standard, metribuzin at all concentrations. Thus, it can be concluded that substituted cinnamic acids and their amide analogues may be developed as potential herbicides.

  6. Using the cre-lox recombination system to assess functional impairment caused by amino acid substitutions in yeast proteins

    Shirley Renee L.

    2004-01-01

    Full Text Available A method was developed to assess the functional significance of a sequence motif in yeast Upf3p, a protein required for nonsense-mediated mRNA decay (NMD. The motif lies at the edge of the Upf3p-Upf2p interaction domain, but at the same time resembles the canonical leucine-rich nuclear export sequence (NES found in proteins that bind Crm1p exportin. To test the function of the putative NES, site-directed mutations that cause substitutions of conserved NES-A residues were first selected to identify hypermorphic alleles. Next, a portable Crm1p-binding NES from HIV-1 Rev protein that functions in yeast was fused en masse to the C-terminus of variant Upf3 proteins using loxP sites recognized by bacterial cre-recombinase. Finally, variant Upf3-Rev proteins that were functional in NMD were selected and examined for the types of amino acid substitutions present in NES-A. The mutational analysis revealed that amino acid substitutions in the Upf3 NES impair both nuclear export and the Upf2p-Upf3p interaction, both of which are required for Upf3p to function in NMD. The method described in this report could be modified for the genetic analysis of a variety of portable protein domains.

  7. Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonica and their substitutes.

    Yuan, Yuan; Wang, Zhouyong; Jiang, Chao; Wang, Xumin; Huang, Luqi

    2014-01-25

    Chlorogenic acids (CGAs) and luteolin are active compounds in Lonicera japonica, a plant of high medicinal value in traditional Chinese medicine. This study provides a comprehensive overview of gene families involved in chlorogenic acid and luteolin biosynthesis in L. japonica, as well as its substitutes Lonicera hypoglauca and Lonicera macranthoides. The gene sequence feature and gene expression patterns in various tissues and buds of the species were characterized. Bioinformatics analysis revealed that 14 chlorogenic acid and luteolin biosynthesis-related genes were identified from the L. japonica transcriptome assembly. Phylogenetic analyses suggested that the function of individual gene could be differentiation and induce active compound diversity. Their orthologous genes were also recognized in L. hypoglauca and L. macranthoides genomic datasets, except for LHCHS1 and LMC4H2. The expression patterns of these genes are different in the tissues of L. japonica, L. hypoglauca and L. macranthoides. Results also showed that CGAs were controlled in the first step of biosynthesis, whereas both steps controlled luteolin in the bud of L. japonica. The expression of LJFNS2 exhibited positive correlation with luteolin levels in L. japonica. This study provides significant information for understanding the functional diversity of gene families involved in chlorogenic acid and the luteolin biosynthesis, active compound diversity of L. japonica and its substitutes, and the different usages of the three species.

  8. The Lys234Arg Substitution in the Enzyme SHV-72 Is a Determinant for Resistance to Clavulanic Acid Inhibition▿

    Mendonça, Nuno; Manageiro, Vera; Robin, Frédéric; Salgado, M. José; Ferreira, Eugénia; Caniça, Manuela; Bonnet, Richard

    2008-01-01

    The new β-lactamase SHV-72 was isolated from clinical Klebsiella pneumoniae INSRA1229, which exhibited the unusual association of resistance to the amoxicillin-clavulanic acid combination (MIC, 64 μg/ml) and susceptibility to cephalosporins, aztreonam, and imipenem. SHV-72 (pI 7.6) harbored the three amino acid substitutions Ile8Phe, Ala146Val, and Lys234Arg. SHV-72 had high catalytic efficiency against penicillins (kcat/Km, 35 to 287 μM−1·s−1) and no activity against oxyimino β-lactams. The concentration of clavulanic acid necessary to inhibit the enzyme activity by 50% was 10-fold higher for SHV-72 than for SHV-1. Molecular-dynamics simulation suggested that the Lys234Arg substitution in SHV-72 stabilized an atypical conformation of the Ser130 side chain, which moved the Oγ atom of Ser130 around 3.5 Å away from the key Oγ atom of the reactive serine (Ser70). This movement may therefore decrease the susceptibility to clavulanic acid by preventing cross-linking between Ser130 and Ser70. PMID:18316518

  9. Supramolecular complex formation of β-cyclodextrin polymer with substituted salicylic acid or 3-hydroxy-2-naphthoic acid and their electrorheological behaviors

    GAO Ziwei; ZHAO Xiaopeng; SUN Ping; SI Gang

    2004-01-01

    According to the chemical design, electrorheological properties of supramolecular complex from β-cyclodextrin polymer (β -CDP) were discussed. Six supramolecular complexes of β-cyclodextrin polymer with substituted salicylic acid and 3-hydroxy-2-naphthoic acid were synthesized by the solid-phase self-assembly method, and their component and structure were characterized by NMR, FT-IR, UV-vis and the fluorescence analysis. Then the electrorheological properties of their suspensions in silicone oil were investigated under DC electric fields. It was found that the yield stresses of these supramolecular complex ER fluids were 7.3-9.8 kPa at 4kV/mm in DC electric field, which were enhanced by 34%-72% compared with that of pure β-CDP. Among them, that of β-CDP/3-hydroxy-2-naphthoic acid ER fluid was the highest. It was also found that the ER effect of supramolecular complexes can be controlled by changing different guests. When the substituted group is at phenyl ring, ER behavior can be slightly adjusted by the different substituted groups, their number as well as their position at phenyl ring. This can be proved by the measurement of dielectric properties.

  10. Amino Acid Substitutions Improve the Immunogenicity of H7N7HA Protein and Protect Mice against Lethal H7N7 Viral Challenge.

    Subaschandrabose Rajesh Kumar

    Full Text Available Avian influenza A H7N7/NL/219/03 virus creates a serious pandemic threat to human health because it can transmit directly from domestic poultry to humans and from human to human. Our previous vaccine study reported that mice when immunized intranasally (i.n with live Bac-HA were protected from lethal H7N7/NL/219/03 challenge, whereas incomplete protection was obtained when administered subcutaneously (s.c due to the fact that H7N7 is a poor inducer of neutralizing antibodies. Interestingly, our recent vaccine studies reported that mice when vaccinated subcutaneously with Bac-HA (H7N9 was protected against both H7N9 (A/Sh2/2013 and H7N7 virus challenge. HA1 region of both H7N7 and H7N9 viruses are differ at 15 amino acid positions. Among those, we selected three amino acid positions (T143, T198 and I211 in HA1 region of H7N7. These amino acids are located within or near the receptor binding site. Following the selection, we substituted the amino acid at these three positions with amino acids found on H7N9HA wild-type. In this study, we evaluate the impact of amino acid substitutions in the H7N7 HA-protein on the immunogenicity. We generated six mutant constructs from wild-type influenza H7N7HA cDNA by site directed mutagenesis, and individually expressed mutant HA protein on the surface of baculovirus (Bac-HAm and compared their protective efficacy of the vaccines with Bac-H7N7HA wild-type (Bac-HA by lethal H7N7 viral challenge in a mouse model. We found that mice immunized subcutaneously with Bac-HAm constructs T143A or T198A-I211V or I211V-T143A serum showed significantly higher hemagglutination inhibition and neutralization titer against H7N7 and H7N9 viruses when compared to Bac-HA vaccinated mice groups. We also observed low level of lung viral titer, negligible weight loss and complete protection against lethal H7N7 viral challenge. Our results indicated that amino acid substitution at position 143 or 211 improve immunogenicity of H7N7HA

  11. Hexanoic acid and polyethylene glycol double grafted amphiphilic chitosan for enhanced gene delivery: influence of hydrophobic and hydrophilic substitution degree.

    Layek, Buddhadev; Haldar, Manas K; Sharma, Gitanjali; Lipp, Lindsey; Mallik, Sanku; Singh, Jagdish

    2014-03-03

    Gene therapy holds immense potential as a future therapeutic strategy for the treatment of numerous genetic diseases which are incurable to date. Nevertheless, safe and efficient gene delivery remains the most challenging aspects of gene therapy. To overcome this difficulty a series of hexanoic acid (HA) and monomethoxy poly(ethylene glycol) (mPEG) double grafted chitosan-based (HPC) nanomicelles were developed as nonviral gene carrier. HPC polymers with various HA and mPEG substitution degrees were synthesized, and their chemical structures were confirmed by (1)H NMR spectroscopy. HPC nanomicelles exhibited excellent blood compatibility and cell viability, as demonstrated by in vitro hemolysis and MTT assay, respectively. The cationic HPC nanomicelles retained the plasmid DNA (pDNA) binding capacity of chitosan and formed stable HPC/pDNA polyplexes with diameters below 200 nm. Both hydrophobic and hydrophilic substitution resulted in suppressed nonspecific protein adsorption on HPC/pDNA polyplexes and increased pDNA dissociation. However, resistance against DNase I degradation was enhanced by HA conjugation while being inhibited by mPEG substitution. Amphiphilic modification resulted in 3-4.5-fold higher cellular uptake in human embryonic kidney 293 cells (HEK 293) mainly through clathrin-mediated pathway. The optimal HPC/pDNA polyplexes displayed 50-fold and 1.2-fold higher gene transfection compared to unmodified chitosan and Fugene, respectively, in HEK 293 cells. Moreover, both the cellular uptake and in vitro transfection study suggested a clear dependence of gene expression on the extent of HA and mPEG substitution. These findings demonstrate that amphiphilic HPC nanomicelles with the proper combination of HA and mPEG substitution could be used as a promising gene carrier for efficient gene therapy.

  12. Durability of Concrete Using Rice Husk Ash as Cement Substitution Exposed To Acid Rain

    I. A. Ahmad

    2014-05-01

    Full Text Available The acidity of rainfall in major areas of Indonesia is under neutral pH. Average pH of rainfall is between 3 and 5. Free lime within concrete will react with acid and cause a decrease in the strength of concrete. A means to anticipate the damage is to reduce the content of free lime within concrete. Silicon oxide contained in rice husk ash can react with free lime to form a new compound that is harder and denser. It became the basis for the use of rice husk ash in concrete mixtures. The mixtures were prepared by replacing 5% and 10% of cement with rice husk ash and the results were compared with a reference mix with 100% cement. This paper presents the results of an experimental investigation on the mechanical characteristics of concrete specimens as durability parameters. Then to evaluate the mechanical characteristics, microstructure test was conducted. The lower the mechanical properties of the concrete, the higher the level of gypsum contained within concrete. The percentage of 5% rice husk ash of the cement weight has a lower compressive strength decrease than the 10% rice husk ash. In addition, the proposed durability model is a model of polynomial equation with two variables.

  13. Generation of novel cationic antimicrobial peptides from natural non-antimicrobial sequences by acid-amide substitution

    Tamada Yasushi

    2011-03-01

    Full Text Available Abstract Background Cationic antimicrobial peptides (CAMPs are well recognized to be promising as novel antimicrobial and antitumor agents. To obtain novel skeletons of CAMPs, we propose a simple strategy using acid-amide substitution (i.e. Glu→Gln, Asp→Asn to confer net positive charge to natural non-antimicrobial sequences that have structures distinct from known CAMPs. The potential of this strategy was verified by a trial study. Methods The pro-regions of nematode cecropin P1-P3 (P1P-P3P were selected as parent sequences. P1P-P3P and their acid-amide-substituted mutants (NP1P-NP3P were chemically synthesized. Bactericidal and membrane-disruptive activities of these peptides were evaluated. Conformational changes were estimated from far-ultraviolet circular dichroism (CD spectra. Results NP1P-NP3P acquired potent bactericidal activities via membrane-disruption although P1P-P3P were not antimicrobial. Far-ultraviolet CD spectra of NP1P-NP3P were similar to those of their parent peptides P1P-P3P, suggesting that NP1P-NP3P acquire microbicidal activity without remarkable conformational changes. NP1P-NP3P killed bacteria in almost parallel fashion with their membrane-disruptive activities, suggesting that the mode of action of those peptides was membrane-disruption. Interestingly, membrane-disruptive activity of NP1P-NP3P were highly diversified against acidic liposomes, indicating that the acid-amide-substituted nematode cecropin pro-region was expected to be a unique and promising skeleton for novel synthetic CAMPs with diversified membrane-discriminative properties. Conclusions The acid-amide substitution successfully generated some novel CAMPs in our trial study. These novel CAMPs were derived from natural non-antimicrobial sequences, and their sequences were completely distinct from any categories of known CAMPs, suggesting that such mutated natural sequences could be a promising source of novel skeletons of CAMPs.

  14. Synthesis of Substituted Thioureas and Their Sulfur Heterocyclic Systems of p-Amino Salicylic Acid as Antimycobacterial Agents

    Mohammed Saleh I. T. Makki

    2013-01-01

    Full Text Available A series of new N,N′-substituted thioureas (2, 6, and 8 and their sulfur heterocycles as thiobarbituric acids (3, 4, and 7, 2-thioxothiazoliodin-4-one (10, thiazolidin-4-one (11, 1,2,4-triazol-5-thione (14, and 1,3,4-thiadiazole (15 of p-Amino salicylic acid (PAS have been synthesized from treatment with dithiocarbazinate (1, 5 and 12 followed by heterocyclization with dimethyl malonate, chloroacetic acid, and/or trifluoroacetic anhydride. The structures of the newly synthesized compounds were substantiated with IR, H1, and C13 NMR spectral data and elementary microanalyses. The in vitro antitubercular activity of synthesized compounds against M. tuberculosis strain H37Rv showed moderate-to-good activity.

  15. A Diffusion Theory Model of Adoption and Substitution for Successive Generations of High-Technology Products

    John A. Norton; Frank M. Bass

    1987-01-01

    This study deals with the dynamic sales behavior of successive generations of high-technology products. New technologies diffuse through a population of potential buyers over time. Therefore, diffusion theory models are related to this demand growth. Furthermore, successive generations of a technology compete with earlier ones, and that behavior is the subject of models of technological substitution. Building upon the Bass (Bass, F. M. 1969. A new-product growth model for consumer durables. M...

  16. Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders--a computational approach.

    Rajith B

    Full Text Available BACKGROUND: A major area of effort in current genomics is to distinguish mutations that are functionally neutral from those that contribute to disease. Single Nucleotide Polymorphisms (SNPs are amino acid substitutions that currently account for approximately half of the known gene lesions responsible for human inherited diseases. As a result, the prediction of non-synonymous SNPs (nsSNPs that affect protein functions and relate to disease is an important task. PRINCIPAL FINDINGS: In this study, we performed a comprehensive analysis of deleterious SNPs at both functional and structural level in the respective genes associated with red blood cell metabolism disorders using bioinformatics tools. We analyzed the variants in Glucose-6-phosphate dehydrogenase (G6PD and isoforms of Pyruvate Kinase (PKLR & PKM2 genes responsible for major red blood cell disorders. Deleterious nsSNPs were categorized based on empirical rule and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for evaluation of protein structure stability. SIGNIFICANCE: We argue here that bioinformatics tools can play an important role in addressing the complexity of the underlying genetic basis of Red Blood Cell disorders. Based on our investigation, we report here the potential candidate SNPs, for future studies in human Red Blood Cell disorders. Current study also demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies. Our approach will present the application of computational tools in understanding functional variation from the perspective of structure, expression, evolution and phenotype.

  17. Memory-Based Simple Heuristics as Attribute Substitution: Competitive Tests of Binary Choice Inference Models.

    Honda, Hidehito; Matsuka, Toshihiko; Ueda, Kazuhiro

    2016-07-20

    Some researchers on binary choice inference have argued that people make inferences based on simple heuristics, such as recognition, fluency, or familiarity. Others have argued that people make inferences based on available knowledge. To examine the boundary between heuristic and knowledge usage, we examine binary choice inference processes in terms of attribute substitution in heuristic use (Kahneman & Frederick, 2005). In this framework, it is predicted that people will rely on heuristic or knowledge-based inference depending on the subjective difficulty of the inference task. We conducted competitive tests of binary choice inference models representing simple heuristics (fluency and familiarity heuristics) and knowledge-based inference models. We found that a simple heuristic model (especially a familiarity heuristic model) explained inference patterns for subjectively difficult inference tasks, and that a knowledge-based inference model explained subjectively easy inference tasks. These results were consistent with the predictions of the attribute substitution framework. Issues on usage of simple heuristics and psychological processes are discussed.

  18. Amino acid substitutions in the thymidine kinase gene of induced acyclovir-resistant herpes simplex virus type 1

    Hussin, Ainulkhir; Nor, Norefrina Shafinaz Md; Ibrahim, Nazlina

    2013-11-01

    Acyclovir (ACV) is an antiviral drug of choice in healthcare setting to treat infections caused by herpes viruses, including, but not limited to genital herpes, cold sores, shingles and chicken pox. Acyclovir resistance has emerged significantly due to extensive use and misuse of this antiviral in human, especially in immunocompromised patients. However, it remains unclear about the amino acid substitutions in thymidine (TK) gene, which specifically confer the resistance-associated mutation in herpes simplex virus. Hence, acyclovir-resistant HSV-1 was selected at high concentration (2.0 - 4.5 μg/mL), and the TK-gene was subjected to sequencing and genotypic characterization. Genotypic sequences comparison was done using HSV-1 17 (GenBank Accesion no. X14112) for resistance-associated mutation determination whereas HSV-1 KOS, HSV-1 473/08 and HSV clinical isolates sequences were used for polymorphism-associated mutation. The result showed that amino acid substitutions at the non-conserved region (UKM-1: Gln34Lys, UKM-2: Arg32Ser & UKM-5: Arg32Cys) and ATP-binding site (UKM-3: Tyr53End & UKM-4: Ile54Leu) of the TK-gene. These discoveries play an important role to extend another dimension to the evolution of acyclovir-resistant HSV-1 and suggest that selection at high ACV concentration induced ACV-resistant HSV-1 evolution. These findings also expand the knowledge on the type of mutations among acyclovir-resistant HSV-1. In conclusion, HSV-1 showed multiple strategies to exhibit acyclovir resistance, including amino acid substitutions in the TK gene.

  19. Identification by random forest method of HLA class I amino acid substitutions associated with lower survival at day 100 in unrelated donor hematopoietic cell transplantation.

    Marino, S R; Lin, S; Maiers, M; Haagenson, M; Spellman, S; Klein, J P; Binkowski, T A; Lee, S J; van Besien, K

    2012-02-01

    The identification of important amino acid substitutions associated with low survival in hematopoietic cell transplantation (HCT) is hampered by the large number of observed substitutions compared with the small number of patients available for analysis. Random forest analysis is designed to address these limitations. We studied 2107 HCT recipients with good or intermediate risk hematological malignancies to identify HLA class I amino acid substitutions associated with reduced survival at day 100 post transplant. Random forest analysis and traditional univariate and multivariate analyses were used. Random forest analysis identified amino acid substitutions in 33 positions that were associated with reduced 100 day survival, including HLA-A 9, 43, 62, 63, 76, 77, 95, 97, 114, 116, 152, 156, 166 and 167; HLA-B 97, 109, 116 and 156; and HLA-C 6, 9, 11, 14, 21, 66, 77, 80, 95, 97, 99, 116, 156, 163 and 173. In all 13 had been previously reported by other investigators using classical biostatistical approaches. Using the same data set, traditional multivariate logistic regression identified only five amino acid substitutions associated with lower day 100 survival. Random forest analysis is a novel statistical methodology for analysis of HLA mismatching and outcome studies, capable of identifying important amino acid substitutions missed by other methods.

  20. Origin of the low temperature excess heat capacity of isotopically substituted acetylsalicylic acid

    Schröder, F.; Winkler, B.; Bauer, J. D.; Haussühl, E.; Rivera Escoto, B.; Tristan López, F.; Avalos Borja, M.; Richter, C.; Ferner, J.

    2011-09-01

    The low temperature heat capacities of single crystals of fully protonated acetylsalicylic acid, measured between 2 K < T < 80 K, have been compared to samples in which the methyl-group was replaced by CD3, CH2D and 13CH3. For the partially methyl-deuterated crystal (CH2D) a significant excess heat capacity was found below T < 40 K with a broad maximum around T ≈ 14 K. The thermodynamic data are explained on the basis of a Schottky model using results obtained in earlier NMR and neutron spectroscopic experiments. In contrast, the excess heat capacity of the fully deuterated compound can be explained by a change of the phonon density of states.

  1. Anti-influenza virus effect of some propolis constituents and their analogues (esters of substituted cinnamic acids).

    Serkedjieva, J; Manolova, N; Bankova, V

    1992-03-01

    The antiviral activity of six synthetic substances, esters of substituted cinnamic acids, identical with or analogous to some of the constituents of the Et2O fraction of propolis was studied in vitro. One of them, isopentyl ferulate, inhibited significantly the infectious activity of influenza virus A/Hong Kong (H3N2) in vitro and the production of hemagglutinins in ovo. By the use of diverse experimental patterns, it was found that the maximal inhibition of viral reproduction was observed when test substances were present in the medium during the whole infectious process.

  2. Amino acid substitutions in the intracellular part of the growth hormone receptor in a patient with the laron syndrome

    Kou, Kou; Lajara, R.; Rotwein, P. (Washington Univ. School of Medicine, St. Louis, MO (United States))

    1993-01-01

    By complementary DNA cloning the authors have identified two amino acid substitutions in the intracellular region of the human GH receptor in a child with growth failure and clinical features of the Laron syndrome. At the second position of codon 422 a G to T transversion changes a cysteine residue to phenylalanine, whereas at the first nucleotide of coden 561 an alteration from C to A leads to the substitution of threonine for proline. Direct analysis of exon 10 of the GH receptor gene showed that both nucleotide substitutions reside on the same chromosome and were inherited from the patient's mother. Evaluation of DNA from 10 additional prospectively recruited children with growth failure and a clinical picture similar to the index case did not reveal any nucleotide alterations in codons 422, 560, or 561. These observations represent the first demonstration of variation within the intracytoplasmic part of the human GH receptor and indicate that mutations occurring at multiple locations within the receptor gene may lead to the same clinical phenotype. 32 refs., 6 figs., 2 tabs.

  3. Effects of Hypoxanthine Substitution in Peptide Nucleic Acids Targeting KRAS2 Oncogenic mRNA Molecules: Theory and Experiment

    Sanders, Jeffrey M.; Wampole, Matthew E.; Chen, Chang-Po; Sethi, Dalip; Singh, Amrita; Dupradeau, François-Yves; Wang, Fan; Gray, Brian D.; Thakur, Mathew L.; Wickstrom, Eric

    2013-01-01

    Genetic disorders can arise from single base substitutions in a single gene. A single base substitution for wild type guanine in the twelfth codon of KRAS2 mRNA occurs frequently to initiate lung, pancreatic, and colon cancer. We have observed single base mismatch specificity in radioimaging of mutant KRAS2 mRNA in tumors in mice by in vivo hybridization with radiolabeled peptide nucleic acid (PNA) dodecamers. We hypothesized that multi-mutant specificity could be achieved with a PNA dodecamer incorporating hypoxanthine, which can form Watson-Crick basepairs with adenine, cytosine, thymine, and uracil. Using molecular dynamics simulations and free energy calculations, we show that hypoxanthine substitutions in PNAs are tolerated in KRAS2 RNA-PNA duplexes where wild type guanine is replaced by mutant uracil or adenine in RNA. To validate our predictions, we synthesized PNA dodecamers with hypoxanthine, and then measured the thermal stability of RNA-PNA duplexes. Circular dichroism thermal melting results showed that hypoxanthine-containing PNAs are more stable in duplexes where hypoxanthine-adenine and hypoxanthine-uracil base pairs are formed than single mismatch duplexes or duplexes containing hypoxanthine-guanine opposition. PMID:23972113

  4. VSMP for Modeling the Biodegradability of Substituted Benzenes Based on Electrotopological State Indices for Atom Types

    LIU Shu-Shen; YIN Da-Qiang; CUI Shi-Hai; WANG Lian-Sheng

    2005-01-01

    The electrotopological state (E-state) index was employed to characterize the structures of 51 substituted benzenes. Eleven E-state indices of the compounds were calculated by the computer program developed in our laboratory. The method for variable selection and modeling based on prediction (VSMP) was used to select an optimal combination of the variables from 11 E-state descriptors. Then the optimal descriptors were employed to model the relationship between the relative biodegradability of the substituted benzenes and their molecular structures. A novel 5-descriptor linear model was developed and the model has a high quality with the correlation coefficient and the root mean square error in estimation step being 0.9378 and 0.35, respectively, and these in leave-one-out cross-validation procedure being 0.9210 and 0.39, respectively.

  5. Production and validation of model iron-tannate dyed textiles for use as historic textile substitutes in stabilisation treatment studies

    Wilson Helen

    2012-05-01

    Full Text Available Abstract Background For millennia, iron-tannate dyes have been used to colour ceremonial and domestic objects shades of black, grey, or brown. Surviving iron-tannate dyed objects are part of our cultural heritage but their existence is threatened by the dye itself which can accelerate oxidation and acid hydrolysis of the substrate. This causes many iron-tannate dyed textiles to discolour and decrease in tensile strength and flexibility at a faster rate than equivalent undyed textiles. The current lack of suitable stabilisation treatments means that many historic iron-tannate dyed objects are rapidly crumbling to dust with the knowledge and value they hold being lost forever. This paper describes the production, characterisation, and validation of model iron-tannate dyed textiles as substitutes for historic iron-tannate dyed textiles in the development of stabilisation treatments. Spectrophotometry, surface pH, tensile testing, SEM-EDX, and XRF have been used to characterise the model textiles. Results On application to textiles, the model dyes imparted mid to dark blue-grey colouration, an immediate tensile strength loss of the textiles and an increase in surface acidity. The dyes introduced significant quantities of iron into the textiles which was distributed in the exterior and interior of the cotton, abaca, and silk fibres but only in the exterior of the wool fibres. As seen with historic iron-tannate dyed objects, the dyed cotton, abaca, and silk textiles lost tensile strength faster and more significantly than undyed equivalents during accelerated thermal ageing and all of the dyed model textiles, most notably the cotton, discoloured more than the undyed equivalents on ageing. Conclusions The abaca, cotton, and silk model textiles are judged to be suitable for use as substitutes for cultural heritage materials in the testing of stabilisation treatments.

  6. Protein-thiol substitution or protein dethiolation by thiol/disulfide exchange reactions: the albumin model.

    Summa, Domenico; Spiga, Ottavia; Bernini, Andrea; Venditti, Vincenzo; Priora, Raffaella; Frosali, Simona; Margaritis, Antonios; Di Giuseppe, Danila; Niccolai, Neri; Di Simplicio, Paolo

    2007-11-01

    Dethiolation experiments of thiolated albumin with thionitrobenzoic acid and thiols (glutathione, cysteine, homocysteine) were carried out to understand the role of albumin in plasma distribution of thiols and disulfide species by thiol/disulfide (SH/SS) exchange reactions. During these experiments we observed that thiolated albumin underwent thiol substitution (Alb-SS-X+RSHAlb-SS-R+XSH) or dethiolation (Alb-SS-X+XSHAlb-SH+XSSX), depending on the different pK(a) values of thiols involved in protein-thiol mixed disulfides (Alb-SS-X). It appeared in these reactions that the compound with lower pK(a) in mixed disulfide was a good leaving group and that the pK(a) differences dictated the kind of reaction (substitution or dethiolation). Thionitrobenzoic acid, bound to albumin by mixed disulfide (Alb-TNB), underwent rapid substitution after thiol addition, forming the corresponding Alb-SS-X (peaks at 0.25-1 min). In turn, Alb-SS-X were dethiolated by the excess nonprotein SH groups because of the lower pK(a) value in mixed disulfide with respect to that of other thiols. Dethiolation of Alb-SS-X was accompanied by formation of XSSX and Alb-SH up to equilibrium levels at 35 min, which were different for each thiol. Structures by molecular simulation of thiolated albumin, carried out for understanding the role of sulfur exposure in mixed disulfides in dethiolation process, evidenced that the sulfur exposure is important for the rate but not for determining the kind of reaction (substitution or dethiolation). Our data underline the contribution of SH/SS exchanges to determine levels of various thiols as reduced and oxidized species in human plasma.

  7. ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping

    Hansen, Christian Skjødt; Østerbye, Thomas; Marcatili, Paolo; Lund, Ole; Buus, Søren

    2017-01-01

    Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes. Using exhaustive amino acid substitution analysis of peptides originating from target antigens, these microarrays can be used to address the specificity of polyclonal antibodies raised against such antigens containing hundreds of epitopes. However, the interpretation of the data provided in such large-scale screenings is far from trivial and in most cases it requires advanced computational and statistical skills. Here, we present an online application for automated identification of linear B cell epitopes, allowing the non-expert user to analyse peptide microarray data. The application takes as input quantitative peptide data of fully or partially substituted overlapping peptides from a given antigen sequence and identifies epitope residues (residues that are significantly affected by substitutions) and visualize the selectivity towards each residue by sequence logo plots. Demonstrating utility, the application was used to identify and address the antibody specificity of 18 linear epitope regions in Human Serum Albumin (HSA), using peptide microarray data consisting of fully substituted peptides spanning the entire sequence of HSA and incubated with polyclonal rabbit anti-HSA (and mouse anti-rabbit-Cy3). The application is made available at: www.cbs.dtu.dk/services/ArrayPitope. PMID:28095436

  8. Self-assembled structure of alkyloxy substituted benzoic acid methyl ester on HOPG:An STM study

    YUAN Qunhui; LU Jun; WAN Lijun; BAI Chunli

    2004-01-01

    Self-assembled structures of 3,4,5-tris-dodecy- loxy benzoic acid methyl ester (E12), 3,4,5-tris-tetradecy- loxy-benzoic acid methyl ester (E14) and their mixture (E12/E14) have been studied on HOPG by scanning tunneling microscopy (STM). Dimer-like patterns induced by dipole-dipole interaction are observed in E12 and E14 monolayers. The molecules form close-packed rows and interdigitate with the alkyl chains in adjacent molecules. The structural differences are proposed to be from the different length of substituted alkyl chains. Owing to similar adsorption energy, phase separation is observed in the E12 and E14 mixed adlayer with different domains.

  9. Infrared study of some 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids. Correlation with MO-calculations

    IVAN O. JURANIC

    2000-06-01

    Full Text Available The IR spectra of a series of 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids (substituent = OH, SH, CH3, CH3S and NH2 were studied from the aspect of the influence of the subsitutent on the polarizability of some bonds, keto-enol tautomerism and hydrogen bond formation. The spectra were taken using solids due to the low solubility of the acids. Theoretical calculations were done using the MNDO-AM1 semiempirical molecular-orbital method. The stabilities of various tautomers were calculated simulating the dielectric continuum using the COSMO facility of the MOPAC program package. Theoretical calculations were made for all the possible tautomers of the 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids. For the most stable isomers, the vibrational spectra were calculated. For the majority of the compounds the most stable isomer was identified having the structure 2-Y-6-oxo-4-carboxy-3H-pyrimidine. Besides this structure, for the 2-amino-, and 2-methyl- derivatives the zwitterionic forms have very similar stability. The 2-hydroxy compound is most stable as the 2,6-dioxo-1H, 3H isomer. The calculated vibrations for the compounds with a single stable structure correlate very well with the experimental frequencies. For the 2-methyl- and 2-amino- compounds the correlation is considerably less satisfactory. The most probable reason for this deviation is the existence of two or more tautomets in equilibrium. The correlation of the measured frequencies and the pKa values of the acids, indicate that the same tautomers exist in the solid state and in the solution.

  10. Design, synthesis and SAR studies of GABA uptake inhibitors derived from 2-substituted pyrrolidine-2-yl-acetic acids.

    Steffan, Tobias; Renukappa-Gutke, Thejavathi; Höfner, Georg; Wanner, Klaus T

    2015-03-15

    In this paper, we disclose the design and synthesis of a series of 2-substituted pyrrolidine-2-yl-acetic acid as core structures and the N-arylalkyl derivatives thereof as potential GABA transport inhibitors. The 2-position in the side chain of pyrrolidine-2-yl-acetic acid derivatives was substituted with alkyl, hydroxy and amino groups to modulate the activity and selectivity to mGAT1 and mGAT4 proteins. SAR studies of the compounds performed for the four mouse GABA transporter proteins (mGAT1-mGAT4) implied significant potencies and subtype selectivities for 2-hydroxy-2-pyrrolidine-2-yl-acetic acid derivatives. The racemate rac-(u)-13c exhibited the highest potency (pIC50 5.67) at and selectivity for mGAT1 in GABA uptake assays. In fact, the potency of rac-(u)-13c at hGAT-1 (pIC50 6.14) was even higher than its potency at mGAT1. These uptake results for rac-(u)-13c are in line with the binding affinities to the aforesaid proteins mGAT1 (pKi 6.99) and hGAT-1 (pKi 7.18) determined by MS Binding Assay based on NO711 as marker quantified by LC-ESI-MS-MS analysis. Interestingly, the 2-hydroxy-2-pyrrolidine-2-yl-acetic acid rac-(u)-13d containing 2-{[tris(4-methoxyphenyl)]methoxy} ethyl group at the nitrogen atom of the pyrrolidine ring showed high potency at mGAT4 and a comparatively better selectivity for this protein (>15 against mGAT3) than the well known mGAT4 uptake inhibitor (S)-SNAP-5114.

  11. Amino Acid Substitutions That Affect Receptor Binding and Stability of the Hemagglutinin of Influenza A/H7N9 Virus

    Schrauwen, Eefje J. A.; Burke, David F.; Rimmelzwaan, Guus F.; Herfst, Sander; Fouchier, Ron A. M.

    2016-01-01

    Receptor-binding preference and stability of hemagglutinin have been implicated as crucial determinants of airborne transmission of influenza viruses. Here, amino acid substitutions previously identified to affect these traits were tested in the context of an A/H7N9 virus. Some combinations of substitutions, most notably G219S and K58I, resulted in relatively high affinity for α2,6-linked sialic acid receptor and acid and temperature stability. Thus, the hemagglutinin of the A/H7N9 virus may adopt traits associated with airborne transmission. PMID:26792744

  12. Response of Substituted Indoleacetic Acids in the Indolo-alpha-pyrone Fluorescence Determination

    Engvild, Kjeld Christensen; Böttger, M.; Kaiser, P.

    1978-01-01

    .-pyrones. Other halogenated indoleacetic acids show between zero and 60% of the fluorescence of IAA. Apparently the concentration of IAA cannot be determined in crude extracts in the presence of 4-chloro- or 5-hydroxy-indoleacetic acid, because separate determinations of each of these compounds are not possible......The method of indolo-.alpha.-pyrone fluorescence-determination of IAA was investigated to study possible interference from 4-chloro-indoleacetic acid and 5-hydroxyindoleacetic acid, which occur naturally. Both compounds show about 40% of the fluorescence of IAA after conversion into their .alpha...

  13. Evaluation of dermal substitute in a novel co-transplantation model with autologous epidermal sheet.

    Guofeng Huang

    Full Text Available The development of more and more new dermal substitutes requires a reliable and effective animal model to evaluate their safety and efficacy. In this study we constructed a novel animal model using co-transplantation of autologous epidermal sheets with dermal substitutes to repair full-thickness skin defects. Autologous epidermal sheets were obtained by digesting the basement membrane (BM and dermal components from rat split-thickness skins in Dispase II solution (1.2 u/ml at 4 °C for 8, 10 and 12 h. H&E, immunohistochemical and live/dead staining showed that the epidermal sheet preserved an intact epidermis without any BM or dermal components, and a high percentage of viable cells (92.10 ± 4.19% and P63 positive cells (67.43 ± 4.21% under an optimized condition. Porcine acellular dermal matrixes were co-transplanted with the autologous epidermal sheets to repair full-thickness skin defects in Sprague-Dawley rats. The epidermal sheets survived and completely re-covered the wounds within 3 weeks. Histological staining showed that the newly formed stratified epidermis attached directly onto the dermal matrix. Inflammatory cell infiltration and vascularization of the dermal matrix were not significantly different from those in the subcutaneous implantation model. Collagen IV and laminin distributed continuously at the epidermis and dermal matrix junction 4 weeks after transplantation. Transmission electron microscopy further confirmed the presence of continuous lamina densa and hemidesmosome structures. This novel animal model can be used not only to observe the biocompatibility of dermal substitutes, but also to evaluate their effects on new epidermis and BM formation. Therefore, it is a simple and reliable model for evaluating the safety and efficacy of dermal substitutes.

  14. 2-substituted thiazolidine-4(R)-carboxylic acids as prodrugs of L-cysteine. Protection of mice against acetaminophen hepatotoxicity

    Nagasawa, H.T.; Goon, D.J.; Muldoon, W.P.; Zera, R.T.

    1984-05-01

    A number of 2-alkyl- and 2-aryl-substituted thiazolidine-4(R)-carboxylic acids were evaluated for their protective effect against hepatotoxic deaths produced in mice by LD/sub 90/ doses of acetaminophen. 2(RS)-Methyl-, 2(RS)-n-propyl-, and 2(RS)-n- pentylthiazolidine -4(R)-carboxylic acids (compounds 1b,d,e, respectively) were nearly equipotent in their protective effect based on the number of surviving animals at 48 h as well as by histological criteria. 2(RS)-Ethyl-, 2(RS)-phenyl-, and 2(RS)-(4-pyridyl)thiazolidine-4(R)-carboxylic acids (compounds 1c,f,g) were less protective. The enantiomer of 1b, viz., 2(RS)- methylthiazolidine -4(S)-carboxylic acid (2b), was totally ineffective in this regard. Thiazolidine-4(R)-carboxylic acid (1a), but not its enantiomer, 2a, was a good substrate for a solubilized preparation of rat liver mitochondrial proline oxidase (K/sub m/ 1.1 x 10(-4) M; V/sub max/ . 5.4 mumol min-1 (mg of protein)-1). Compound 1b was not a substrate for proline oxidase but dissociated to L-cysteine in this system. At physiological pH and temperature, the hydrogens on the methyl group of 1b underwent deuterium exchange with solvent D/sub 2/O (k1 . 2.5 X 10(-5) s), suggesting that opening of the thiazolidine ring must have taken place. Indeed, 1b labeled with /sup 14/C in the 2 and methyl positions was rapidly metabolized by the rat to produce /sup 14/CO/sub 2/, 80% of the dose being excreted in this form in the expired air after 24 h. It is suggested that these 2-substituted thiazolidine-4(R)-carboxylic acids are prodrugs of L-cysteine that liberate this sulfhydryl amino acid in vivo by nonenzymatic ring opening, followed by solvolysis.

  15. Substitution and price elasticity estimates using inter-countrypooled data in a translog cost model

    Roy, Joyashree; Sanstad, Alan H.; Sathaye, Jayant A.; Khaddaria,Raman

    2006-06-01

    Pooled data across several developing countries and the U.S. were used to estimate long-run substitution and price elasticities ina translog framework for the paper, iron and steel, and aggregatemanufacturing industries. While the quality of the estimates variesacross the several industry-specific models, the results suggest highervalues for these elasticities than appear commonly used in integratedassessment models. Estimates of own-price elasticities of energy rangefrom - 0.80 to - 1.76 and are comparable to estimates from previouseconometric studies in the context of developed countries (- 0.77 to -0.87). Substitution elasticities show wider variation across countriesand industries. For energy and capital they range from -1.96 to 9.80, forlabor and energy from 2.61 to 7.11, and for energy and material from -0.26 to 2.07.

  16. Fast Fourier Transform-based Support Vector Machine for Subcellular Localization Prediction Using Different Substitution Models

    2007-01-01

    There are approximately 109 proteins in a cell. A hotspot in bioinformatics is how to identify a protein's subcellular localization, if its sequence is known. In this paper, a method using fast Fourier transform-based support vector machine is developed to predict the subcellular localization of proteins from their physicochemical properties and structural parameters. The prediction accuracies reached 83% in prokaryotic organisms and 84% in eukaryotic organisms with the substitution model of the c-p-v matrix (c, composition; p, polarity; and v, molecular volume). The overall prediction accuracy was also evaluated using the "leave-one-out" jackknife procedure. The influence of the substitution model on prediction accuracy has also been discussed in the work. The source code of the new program is available on request from the authors.

  17. An efficient Biginelli one-pot synthesis of new benzoxazole-substituted dihydropyrimidinones and thiones catalysed by trifluoro acetic acid under solvent-free conditions

    D.Shobha; M.Adharvana Chari; K.H.Ahn

    2009-01-01

    An efficient synthesis of benzoxazole-substituted 3,4-dihydropyrimidinones(DHPMs)using trifluoro acetic acid as the catalyst for the first time from an aldehyde,β-keto ester and benzoxazole-substituted urea/thiourea under solvent-free conditions is described.Compared to the classical Biginelli reaction conditions,this new method consistently has the advantage of excellent yields(80-91%)and short reaction time(40-130 min)at reflux temperature.

  18. 40 CFR 721.10045 - Diazotized substituted heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel...

    2010-07-01

    ... coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (generic). 721.10045... derivative, nickel complex, alkaline salt (generic). (a) Chemical substance and significant new uses subject... heteromonocycle coupled with naphthalene sulfonic acid derivative, nickel complex, alkaline salt (PMN P-02-737)...

  19. An environmentally benign one pot synthesis of substituted quinolines catalysed by fluoroboric acid based ionic liquid

    A Rajendran; C Karthikeyan; K Rajathi; D Ragupathy

    2012-07-01

    Organic synthesis generally required large amount of solvent, avoiding the use of organic solvents in synthesis is a paradigm shift directed at developing more benign chemistry, and with ionic liquids surprisingly can lead to access to new compounds. An elegant one-pot synthesis of quinoline derivatives has been achieved by reaction of substituted anilines with -ketoester at 60°C in ethanol using an ionic liquid [Et3NH]+[BF4]−as catalyst. All the reactions gave products with high degree of purity and excellent yield (78-93%) within the shorter span of time (20-65 min) than those reactions with conventional methods. The screening of solvents as well as the reuse of ionic liquid has been evaluated. The structure of the products has been elucidated by spectral and analytical data. The present scope and potential economic impact of the reaction are demonstrated by the synthesis of substituted quinolines. Remaining challenges and future perspectives of the new transformation are discussed.

  20. A Cornea Substitute Derived from Fish Scale: 6-Month Followup on Rabbit Model

    Fei Yuan; Liyan Wang; Chien-Chen Lin; Cheng-Hung Chou; Lei Li

    2014-01-01

    A fish scale-derived cornea substitute (Biocornea) is proposed as an alternative for human donor corneal tissue. We adopt a regenerative medicine approach to design a primary alternative to the use of fish scale for restoring sight by corneal replacement. Biocornea with corneal multilayer arrangement collagen was implanted to rabbits by pocket implantation. Our study demonstrated the safety and detailed morphologic and physiologic results from the 6 months of followup of rabbit model. In the ...

  1. Evaporation of methyl- and dimethyl-substituted malonic, succinic, glutaric and adipic acid particles at ambient temperatures

    Mønster, Jacob Garbrecht; Rosenørn, Thomas; Svenningsson, Birgitta

    2004-01-01

    Evaporation; organic aerosols; vapor pressure; dicarboxylic acid; maonic acid; succinic acid; glutaric acid; adipic acid......Evaporation; organic aerosols; vapor pressure; dicarboxylic acid; maonic acid; succinic acid; glutaric acid; adipic acid...

  2. Systematic methodology for the development of biocatalytic hydrogen-borrowing cascades: application to the synthesis of chiral α-substituted carboxylic acids from α-substituted α,β-unsaturated aldehydes.

    Knaus, Tanja; Mutti, Francesco G; Humphreys, Luke D; Turner, Nicholas J; Scrutton, Nigel S

    2015-01-07

    Ene-reductases (ERs) are flavin dependent enzymes that catalyze the asymmetric reduction of activated carbon-carbon double bonds. In particular, α,β-unsaturated carbonyl compounds (e.g. enals and enones) as well as nitroalkenes are rapidly reduced. Conversely, α,β-unsaturated esters are poorly accepted substrates whereas free carboxylic acids are not converted at all. The only exceptions are α,β-unsaturated diacids, diesters as well as esters bearing an electron-withdrawing group in α- or β-position. Here, we present an alternative approach that has a general applicability for directly obtaining diverse chiral α-substituted carboxylic acids. This approach combines two enzyme classes, namely ERs and aldehyde dehydrogenases (Ald-DHs), in a concurrent reductive-oxidative biocatalytic cascade. This strategy has several advantages as the starting material is an α-substituted α,β-unsaturated aldehyde, a class of compounds extremely reactive for the reduction of the alkene moiety. Furthermore no external hydride source from a sacrificial substrate (e.g. glucose, formate) is required since the hydride for the first reductive step is liberated in the second oxidative step. Such a process is defined as a hydrogen-borrowing cascade. This methodology has wide applicability as it was successfully applied to the synthesis of chiral substituted hydrocinnamic acids, aliphatic acids, heterocycles and even acetylated amino acids with elevated yield, chemo- and stereo-selectivity. A systematic methodology for optimizing the hydrogen-borrowing two-enzyme synthesis of α-chiral substituted carboxylic acids was developed. This systematic methodology has general applicability for the development of diverse hydrogen-borrowing processes that possess the highest atom efficiency and the lowest environmental impact.

  3. Development of QSAR Model of substituted Benzene Sulphonamide using Multiple Regression Analysis

    R.G.Varma

    2014-01-01

    Full Text Available In continuation of our earlier work in this paper we studied 50 substituted Benzenesulphonamide using substituent nanofluorobutyl sulphonyl chloride (C4F9SO2Cl and pentafluoro benzene sulphonyl chloride (C6F5SO2Cl Accordingly we have development QSAR model of studied compounds. These models were derived using the parameters Balaban Index, Balaban-type index,(Jhetz, Jhetm, Jhetv, Jhete, Jhetp Balaban related index (F,G. and Randic connectivity index (χ1. The best suitable model is predicted on the basis of Maximum-R2 (R-squared.

  4. Supply Chain Modeling for Fluorspar and Hydrofluoric Acid and Implications for Further Analyses

    2015-04-01

    analysis. 15. SUBJECT TERMS supply chain , model, fluorspar, hydrofluoric acid, shortfall, substitution, Defense Logistics Agency, National Defense...unlimited. IDA Document D-5379 Log: H 15-000099 INSTITUTE FOR DEFENSE ANALYSES 4850 Mark Center Drive Alexandria, Virginia 22311-1882 Supply Chain ...E F E N S E A N A L Y S E S IDA Document D-5379 D. Sean Barnett Jerome Bracken Supply Chain Modeling for Fluorspar and Hydrofluoric Acid and

  5. l-dehydroascorbic acid can substitute l-ascorbic acid as dietary vitamin C source in guinea pigs

    Henriette Frikke-Schmidt

    2016-04-01

    Full Text Available Vitamin C deficiency globally affects several hundred million people and has been associated with increased morbidity and mortality in numerous studies. In this study, bioavailability of the oxidized form of vitamin C (l-dehydroascorbic acid or DHA—commonly found in vitamin C containing food products prone to oxidation—was studied. Our aim was to compare tissue accumulation of vitamin C in guinea pigs receiving different oral doses of either ascorbate or DHA. In all tissues tested (plasma, liver, spleen, lung, adrenal glands, kidney, muscle, heart, and brain, only sporadic differences in vitamin C accumulation from ascorbate or DHA were observed except for the lowest dose of DHA (0.25 mg/ml in the drinking water, where approximately half of the tissues had slightly yet significantly less vitamin C accumulation than from the ascorbate source. As these results contradicted data from rats, we continued to explore the ability to recycle DHA in blood, liver and intestine in guinea pigs, rats and mice. These investigations revealed that guinea pigs have similar recycling capacity in red blood cells as observed in humans, while rats and mice do not have near the same ability to reduce DHA in erythrocytes. In liver and intestinal homogenates, guinea pigs also showed a significantly higher ability to recycle DHA compared to rats and mice. These data demonstrate that DHA in guinea pigs—as in humans—is almost as effective as ascorbate as vitamin C source when it comes to taking up and storing vitamin C and further suggest that the guinea pig is superior to other rodents in modeling human vitamin C homeostasis.

  6. L-dehydroascorbic acid can substitute l-ascorbic acid as dietary vitamin C source in guinea pigs.

    Frikke-Schmidt, Henriette; Tveden-Nyborg, Pernille; Lykkesfeldt, Jens

    2016-04-01

    Vitamin C deficiency globally affects several hundred million people and has been associated with increased morbidity and mortality in numerous studies. In this study, bioavailability of the oxidized form of vitamin C (l-dehydroascorbic acid or DHA)-commonly found in vitamin C containing food products prone to oxidation-was studied. Our aim was to compare tissue accumulation of vitamin C in guinea pigs receiving different oral doses of either ascorbate or DHA. In all tissues tested (plasma, liver, spleen, lung, adrenal glands, kidney, muscle, heart, and brain), only sporadic differences in vitamin C accumulation from ascorbate or DHA were observed except for the lowest dose of DHA (0.25mg/ml in the drinking water), where approximately half of the tissues had slightly yet significantly less vitamin C accumulation than from the ascorbate source. As these results contradicted data from rats, we continued to explore the ability to recycle DHA in blood, liver and intestine in guinea pigs, rats and mice. These investigations revealed that guinea pigs have similar recycling capacity in red blood cells as observed in humans, while rats and mice do not have near the same ability to reduce DHA in erythrocytes. In liver and intestinal homogenates, guinea pigs also showed a significantly higher ability to recycle DHA compared to rats and mice. These data demonstrate that DHA in guinea pigs-as in humans-is almost as effective as ascorbate as vitamin C source when it comes to taking up and storing vitamin C and further suggest that the guinea pig is superior to other rodents in modeling human vitamin C homeostasis.

  7. Asymmetric synthesis of enantiomerically and diastereoisomerically enriched 4-[F or Br]-substituted glutamic acids.

    Belokon, Yuri N; Maleev, Victor I; Savel'eva, Tatiana F; Moskalenko, Margarita A; Pripadchev, Dmitri A; Khrustalev, Victor N; Saghiyan, Ashot S

    2010-11-01

    A novel simple synthetic protocol for the preparation of both (2S,4R)- and (2S,4S)-FGlu, applying Michael addition of methyl α-fluoroacrylate to a NiII complex of glycine Schiff base with BPB, was elaborated. In addition, same reaction of mentioned complex with ethyl α-bromoacrylate leads to the NiII complex of the Schiff base of BPB with (2S,4R)-4-bromo-glutamic acid monoester, that can be transformed into the corresponding complexes of 1-aminocyclopropane-1,2-dicarboxylic acid. The decomposition of the diastereoisomerically pure complexes leads to corresponding enantiomerically enriched (ee>98%) amino acids.

  8. A single amino acid substitution in the group 1 Trypanosoma brucei gambiense haptoglobin-hemoglobin receptor abolishes TLF-1 binding.

    E DeJesus

    Full Text Available Critical to human innate immunity against African trypanosomes is a minor subclass of human high-density lipoproteins, termed Trypanosome Lytic Factor-1 (TLF-1. This primate-specific molecule binds to a haptoglobin-hemoglobin receptor (HpHbR on the surface of susceptible trypanosomes, initiating a lytic pathway. Group 1 Trypanosoma brucei gambiense causes human African Trypanosomiasis (HAT, escaping TLF-1 killing due to reduced uptake. Previously, we found that group 1 T. b. gambiense HpHbR (TbgHpHbR mRNA levels were greatly reduced and the gene contained substitutions within the open reading frame. Here we show that a single, highly conserved amino acid in the TbgHpHbR ablates high affinity TLF-1 binding and subsequent endocytosis, thus evading TLF-1 killing. In addition, we show that over-expression of TbgHpHbR failed to rescue TLF-1 susceptibility. These findings suggest that the single substitution present in the TbgHpHbR directly contributes to the reduced uptake and resistance to TLF-1 seen in these important human pathogens.

  9. NCA nucleophilic radiofluorination on substituted benzaldehydes for the preparation of [18F]fluorinated aromatic amino acids

    Wadsak, Wolfgang [Department of Nuclear Medicine, Medical University of Vienna (Austria)]. E-mail: wolfgang.wadsak@meduniwien.ac.at; Wirl-Sagadin, Barbara [Department of Nuclear Medicine, Medical University of Vienna (Austria); Department of Inorganic Chemistry, University of Vienna (Austria); Mitterhauser, Markus [Department of Nuclear Medicine, Medical University of Vienna (Austria); Department of Pharmaceutical Technology and Biopharmaceuticals, University of Vienna (Austria); Hospital Pharmacy of the General Hospital of Vienna (Austria); Mien, Leonhard-Key [Department of Nuclear Medicine, Medical University of Vienna (Austria); Department of Pharmaceutical Technology and Biopharmaceuticals, University of Vienna (Austria); Department of Psychiatry, Medical University of Vienna (Austria); Ettlinger, Dagmar E. [Department of Nuclear Medicine, Medical University of Vienna (Austria); Keppler, Bernhard K. [Department of Inorganic Chemistry, University of Vienna (Austria); Dudczak, Robert [Department of Nuclear Medicine, Medical University of Vienna (Austria); Kletter, Kurt [Department of Nuclear Medicine, Medical University of Vienna (Austria)

    2006-03-15

    Nucleophilic aromatic substitution is a challenging task in radiochemistry. Therefore, a thorough evaluation and optimisation of this step is needed to provide a satisfactory tool for the routine preparation of [{sup 18}F]fluorinated aromatic amino acids. Two methods, already proposed elsewhere, were evaluated and improved. The yields for the radiofluorination were increased whereas activity loss during solid phase extraction was observed. Radiochemical yields for the two methods were 92.7{+-}5.5% (method 1) and 92.1{+-}12.3% (method 2) for conversion and 11.1{+-}2.8% (method 1) and 34.8{+-}0.6% (method 2) for purification, respectively. In total, we demonstrate an optimised method for the preparation of this important class of [{sup 18}F]fluorinated synthons for PET.

  10. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes.

    Yang, Ziheng; Swanson, Willie J

    2002-01-01

    The nonsynonymous to synonymous substitution rate ratio (omega = d(N)/d(S)) provides a sensitive measure of selective pressure at the protein level, with omega values 1 indicating purifying selection, neutral evolution, and diversifying selection, respectively. Maximum likelihood models of codon substitution developed recently account for variable selective pressures among amino acid sites by employing a statistical distribution for the omega ratio among sites. Those models, called random-sites models, are suitable when we do not know a priori which sites are under what kind of selective pressure. Sometimes prior information (such as the tertiary structure of the protein) might be available to partition sites in the protein into different classes, which are expected to be under different selective pressures. It is then sensible to use such information in the model. In this paper, we implement maximum likelihood models for prepartitioned data sets, which account for the heterogeneity among site partitions by using different omega parameters for the partitions. The models, referred to as fixed-sites models, are also useful for combined analysis of multiple genes from the same set of species. We apply the models to data sets of the major histocompatibility complex (MHC) class I alleles from human populations and of the abalone sperm lysin genes. Structural information is used to partition sites in MHC into two classes: those in the antigen recognition site (ARS) and those outside. Positive selection is detected in the ARS by the fixed-sites models. Similarly, sites in lysin are classified into the buried and solvent-exposed classes according to the tertiary structure, and positive selection was detected at the solvent-exposed sites. The random-sites models identified a number of sites under positive selection in each data set, confirming and elaborating the results of the fixed-sites models. The analysis demonstrates the utility of the fixed-sites models, as well as

  11. Characterization of the inflammatory response to four commercial bone graft substitutes using a murine biocompatibility model

    Markel DC

    2012-01-01

    Full Text Available David C Markel1, S Trent Guthrie2, Bin Wu3, Zheng Song4, Paul H Wooley41Department of Orthopaedics, Providence Hospital and Medical Centers, Southfield, MI, 2Henry Ford Hospital, Detroit, MI, 3Department of Biomedical Engineering, Wayne State University, Detroit, MI, 4Orthopaedic Research Institute, Wichita, KS, USAAbstract: Bone grafting is utilized in nearly all orthopedic subspecialties and in most anatomic regions. Bone graft substitutes have the potential to offer similar efficacy as autogenous grafts without the morbidity of harvest. Several studies have noted the efficacy of new-generation bone substitute products, but few studies have evaluated their safety. This study characterizes and quantifies the inflammatory reaction to four different commercially available bone graft substitutes, which were examined using the in vivo murine air pouch biocompatibility model. One coralline hydroxyapatite product was chosen as an example of a purely osteoconductive material. Three demineralized bone matrix products were chosen to represent products that are both osteoconductive and osteoinductive. Samples were implanted in a murine air pouch and harvested after 14 days in situ. Pouch fluid was extracted, mRNA isolated, and reverse transcription polymerase chain reactions carried out to detect interleukin-1 gene expression as a marker for inflammation. In addition, multiple histological characteristics were examined to quantify cellular responses to the implanted materials. All bone graft substitutes induced a significant inflammatory response compared with negative controls. Histology and polymerase chain reaction data indicated that the level of inflammatory reaction was elevated in materials with a higher demineralized bone matrix to carrier proportion. The hydroxyapatite product generated a low inflammatory reaction. In conclusion, this study used an in vivo model of biocompatibility to demonstrate that a significant inflammatory reaction occurs

  12. Enantiopure cyclic O-substituted phenylphosphonothioic acid: synthesis and chirality-recognition ability.

    Ribeiro, Nigel; Kobayashi, Yuka; Maeda, Jin; Saigo, Kazuhiko

    2011-07-01

    As a new acidic selector (resolving agent), we synthesized an enantiopure O-alkyl phenylphosphonothioic acid with a seven-membered ring ((R)-5), which was designed on the basis of the results for the enantioseparation of 1-arylethylamine derivatives with acyclic O-ethyl phenylphosphonothioic acid (I). The phosphonothioic acid (R)-5 showed unique chirality-recognition ability in the enantioseparation of 1-naphthylethylamine derivatives, aliphatic secondary amines, and amino alcohols; the ability was complementary to that of I. The X-ray crystallographic analyses of the less- and more-soluble diastereomeric salts showed that hydrogen-bonding networks in the salt crystals are 2(1) -column-type with a single exception which is cluster-type. In the cases of the 2(1) -column-type crystals, stability of the crystals is firstly governed by hydrogen bonds to form a 2(1) -column and secondly determined by intra-columnar T-shaped CH/π interaction(s), intra-columnar hydrogen bond(s), inter-columnar van der Waals interaction and/or inter-columnar T-shaped CH/π interaction(s). In contrast, the cluster-type salt crystal is stabilized by the assistance of inter-cluster T-shaped CH/π and van der Waals interactions. To realize still more numbers of intra- and inter-columnar and -cluster T-shaped CH/π interactions, the seven-membered ring of (R)-5 plays a considerable role.

  13. Pleiotropic effects of hemagglutinin amino acid substitutions of H5 influenza escape mutants

    Rudneva, Irina A.; Timofeeva, Tatiana A.; Ignatieva, Anna V.; Shilov, Aleksandr A.; Krylov, Petr S. [D.I. Ivanovsky Institute of Virology, 123098 Moscow (Russian Federation); Ilyushina, Natalia A., E-mail: Natalia.Ilyushina@fda.hhs.gov [FDA CDER, 29 Lincoln Drive, Bethesda, MD 20892 (United States); Kaverin, Nikolai V., E-mail: nik.kaverin@gmail.com [D.I. Ivanovsky Institute of Virology, 123098 Moscow (Russian Federation)

    2013-12-15

    In the present study we assessed pleiotropic characteristics of the antibody-selected mutations. We examined pH optimum of fusion, temperatures of HA heat inactivation, and in vitro and in vivo replication kinetics of the previously obtained influenza H5 escape mutants. Our results showed that HA1 N142K mutation significantly lowered the pH of fusion optimum. Mutations of the escape mutants located in the HA lateral loop significantly affected H5 HA thermostability (P<0.05). HA changes at positions 131, 144, 145, and 156 and substitutions at positions 131, 142, 145, and 156 affected the replicative ability of H5 escape mutants in vitro and in vivo, respectively. Overall, a co-variation between antigenic specificity and different HA phenotypic properties has been demonstrated. We believe that the monitoring of pleiotropic effects of the HA mutations found in H5 escape mutants is essential for accurate prediction of mutants with pandemic potential. - Highlights: • HA1 N142K mutation significantly lowered the pH of fusion optimum. • Mutations located in the HA lateral loop significantly affected H5 HA thermostability. • HA changes at positions 131, 142, 144, 145, and 156 affected the replicative ability of H5 mutants. • Acquisition of glycosylation site could lead to the emergence of multiple pleiotropic effects.

  14. Single amino acid substitutions on the needle tip protein IpaD increased Shigella virulence.

    Meghraoui, Alaeddine; Schiavolin, Lionel; Allaoui, Abdelmounaaïm

    2014-07-01

    Infection of colonic epithelial cells by Shigella is associated with the type III secretion system, which serves as a molecular syringe to inject effectors into host cells. This system includes an extracellular needle used as a conduit for secreted proteins. Two of these proteins, IpaB and IpaD, dock at the needle tip to control secretion and are also involved in the insertion of a translocation pore into host cell membrane allowing effector delivery. To better understand the function of IpaD, we substituted thirteen residues conserved among homologous proteins in other bacterial species. Generated variants were tested for their ability to surface expose IpaB and IpaD, to control secretion, to insert the translocation pore, and to invade host cells. In addition to a first group of seven ipaD variants that behaved similarly to the wild-type strain, we identified a second group with mutations V314D and I319D that deregulated secretion of all effectors, but remained fully invasive. Moreover, we identified a third group with mutations Y153A, T161D, Q165L and Y276A, that exhibited increased levels of translocators secretion, pore formation, and cell entry. Altogether, our results offer a better understanding of the role of IpaD in the control of Shigella virulence.

  15. A Cornea Substitute Derived from Fish Scale: 6-Month Followup on Rabbit Model

    Fei Yuan

    2014-01-01

    Full Text Available A fish scale-derived cornea substitute (Biocornea is proposed as an alternative for human donor corneal tissue. We adopt a regenerative medicine approach to design a primary alternative to the use of fish scale for restoring sight by corneal replacement. Biocornea with corneal multilayer arrangement collagen was implanted to rabbits by pocket implantation. Our study demonstrated the safety and detailed morphologic and physiologic results from the 6 months of followup of rabbit model. In the peripheral Biocornea, the collagen fibrils were arranged in reticular fashion. Slit lamp examination showed that haze and an ulcer were not observed in all groups at 3 months postoperatively while all corneas with Biocornea were clear at both 3 months and 6 months postoperatively. The interface of Biocornea and stromal tissue were filled successfully and without observable immune cells at postoperative day 180. Moreover, the Biocornea was not dissolved and degenerated but remained transparent and showed no apparent fragmentation. Our study demonstrated that the Biocornea derived from fish scale as a good substitute had high biocompatibility and support function after a long-term evaluation. This revealed that the new approach of using Biocornea may yield an ideal artificial cornea substitute for long-term inlay placement.

  16. Syntheses of 2- or 6-Substituted Chromones and Chromone Ring-opening Reaction in Polyphosphoric Acid

    HE Xun-gui; YOU Qi-dong; LI Zhi-yu

    2004-01-01

    In an attempt to find new antitumor agents, a novel class of chromone compounds with a benzimidazole or a benzoxazole ring in positions 2 or 6 were synthesized via condensation in polyphosphoric acid(PPA) by using chromone acids as the starting materials. During the preparation process, it was found that PPA could cleave the chromone ring to produce a ring-opening compound(6). The molar ratio of the chromone compound(5) to the ring-opening compound(6) varied with the change of reaction temperature and time. Based on MTT protocol, the antitumor activity of each of the compounds obtained was evaluated against three human cancer cell lines: KB(oral epidermal), A2780(ovary) and Bel7402(liver). The IC50 varied from 54.7 μmol/L to more than 180 μmol/L.

  17. Mechanism of Oxidation of (p-Substituted Phenylthioacetic Acids with N-Bromophthalimide

    N. M. I. Alhaji

    2011-01-01

    Full Text Available The kinetics of oxidation of (phenylthioacetic acid (PTAA by N-Bromophthalimide (NBP in acetonitrile-water solvent mixture at 298 K in the presence of perchloric acid has been followed potentiometrically. The reaction is first-order each in NBP and PTAA and inverse fractional-order in H+. Also, it has been found that the reaction rate is not affected by changes in ionic strength of the reaction medium or by the addition of chemicals such as phthalimide, acrylonitrile and potassium bromide. However, an increase in the water content of the solvent mixture causes an increase in the rate of reaction. These observations have been well analyzed in favour of a SN2-type mechanism, involving NBP itself as the reactive species. Effect of substituents on the reaction rate has been analysed by employing various (p-sustituted phenylthioacetic acids. The electron-releasing substituent in the phenyl ring of PTAA accelerates the reaction rate while the electron-withdrawing substituent retards the rate. The excellently linear Hammett plot yields a large negative ρ value, supporting the involvement a bromosulphonium ion intermediate in the rate-determining step.

  18. Design, synthesis and biological evaluation of 2-(substituted phenyl)thiazolidine-4-carboxylic acid derivatives as novel tyrosinase inhibitors.

    Ha, Young Mi; Park, Yun Jung; Lee, Ji Yeon; Park, Daeui; Choi, Yeon Ja; Lee, Eun Kyeong; Kim, Ji Min; Kim, Jin-Ah; Park, Ji Young; Lee, Hye Jin; Moon, Hyung Ryong; Chung, Hae Young

    2012-02-01

    Herein we describe the design, synthesis and biological activities of 2-(substituted phenyl)thiazolidine-4-carboxylic acid derivatives as novel tyrosinase inhibitors. The target compounds 2a-2j were designed and synthesized from the structural characteristics of N-phenylthiourea, tyrosinase inhibitor and tyrosine, and l-DOPA, the natural substrates of tyrosinase. Among them, (2R/S,4R)-2-(2,4-dimethoxyphenyl)thiazolidine-4-carboxylic acid (2g) caused the greatest inhibition 66.47% at 20 μM of l-DOPA oxidase activity of mushroom tyrosinase. Kinetic analysis of tyrosinase inhibition revealed that 2g is a competitive inhibitor. We predicted the tertiary structure of tyrosinase, and simulated the docking of mushroom tyrosinase with 2g. These results suggest that the binding affinity of 2g with tyrosinase is high. Also, 2g effectively inhibited tyrosinase activity and reduced melanin levels in B16 cells treated with α-MSH. These data strongly suggest that 2g can suppress the production of melanin via the inhibition of tyrosinase activity.

  19. Amino acid substitution in NPC1 that abolishes cholesterol binding reproduces phenotype of complete NPC1 deficiency in mice

    Xie, Xuefen; Brown, Michael S.; Shelton, John M.; Richardson, James A.; Goldstein, Joseph L.; Liang, Guosheng

    2011-01-01

    Substitution mutations in adjacent amino acids of the N-terminal domain of NPC1, a lysosomal membrane protein, abolish its cholesterol binding activity and impair its ability to export cholesterol from lysosomes of cultured cells lacking npc1 [Kwon HJ, et al. (2009) Cell 137:1213–1224]. Here, we show that the same two mutations (proline-202 and phenylalanine-203, both changed to alanine) reproduce the phenotype of complete NPC1 deficiency when knocked into the mouse npc1 gene by homologous recombination. Homozygous npc1pf/pf mice exhibited neurodegeneration beginning at day 49 and died at a median age of 84 d, as previously reported for mice that lack npc1. Liver and other organs of the npc1pf/pf mice accumulated excess cholesterol in lysosomes. In liver, mRNAs encoding several lysosomal proteins were elevated, including NPC1 and NPC2 and several digestive enzymes (acid lipase, β-glucuronidase, and cathepsins B and D). Weekly treatment with hydroxypropyl-β-cyclodextrin (HPCD) beginning at 7 wk reduced hepatic cholesterol accumulation and diminished the lysosomal mRNAs. We conclude that the cholesterol binding site in the N-terminal domain of NPC1 is essential for cholesterol export from lysosomes in living animals as it is in cultured cells. The HPCD-mediated reduction of excess lysosomal enzymes may contribute to the ability of this drug to delay the progression of NPC disease in mice. PMID:21896731

  20. In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution.

    Kaminski, Pierre Alexandre; Dacher, Priscilla; Dugué, Laurence; Pochet, Sylvie

    2008-07-18

    Nucleoside 2'-deoxyribosyltransferases catalyze the transfer of 2-deoxyribose between bases and have been widely used as biocatalysts to synthesize a variety of nucleoside analogs. The genes encoding nucleoside 2'-deoxyribosyltransferase (ndt) from Lactobacillus leichmannii and Lactobacillus fermentum underwent random mutagenesis to select variants specialized for the synthesis of 2',3'-dideoxynucleosides. An Escherichia coli strain, auxotrophic for uracil and unable to use 2',3'-dideoxyuridine, cytosine, and 2',3'-dideoxycytidine as a source of uracil was constructed. Randomly mutated lactobacilli ndt libraries from two species, L. leichmannii and L. fermentum, were screened for the production of uracil with 2',3'-dideoxyuridine as a source of uracil. Several mutants suitable for the synthesis of 2',3'-dideoxynucleosides were isolated. The nucleotide sequence of the corresponding genes revealed a single mutation (G --> A transition) leading to the substitution of a small aliphatic amino acid by a nucleophilic one, A15T (L. fermentum) or G9S (L. leichmannii), respectively. We concluded that the "adaptation" of the nucleoside 2'-deoxyribosyltransferase activity to 2,3-dideoxyribosyl transfer requires an additional hydroxyl group on a key amino acid side chain of the protein to overcome the absence of such a group in the corresponding substrate. The evolved proteins also display significantly improved nucleoside 2',3'-didehydro-2',3'-dideoxyribosyltransferase activity.

  1. QSAR modeling for anti-human African trypanosomiasis activity of substituted 2-Phenylimidazopyridines

    Masand, Vijay H.; El-Sayed, Nahed N. E.; Mahajan, Devidas T.; Mercader, Andrew G.; Alafeefy, Ahmed M.; Shibi, I. G.

    2017-02-01

    In the present work, sixty substituted 2-Phenylimidazopyridines previously reported with potent anti-human African trypanosomiasis (HAT) activity were selected to build genetic algorithm (GA) based QSAR models to determine the structural features that have significant correlation with the activity. Multiple QSAR models were built using easily interpretable descriptors that are directly associated with the presence or the absence of a structural scaffold, or a specific atom. All the QSAR models have been thoroughly validated according to the OECD principles. All the QSAR models are statistically very robust (R2 = 0.80-0.87) with high external predictive ability (CCCex = 0.81-0.92). The QSAR analysis reveals that the HAT activity has good correlation with the presence of five membered rings in the molecule.

  2. Cellulose-Sulfuric Acid as an Efficient Biosupported Catalyst in One-Pot Synthesis of Novel Heteroaryl Substituted 1,4-Dihydropyridines

    Manouchehr Mamaghani

    2013-01-01

    Full Text Available An efficient method for the synthesis of new heteroaryl substituted dihydropyridine derivatives via a one-pot four-component coupling reaction of heteroaldehyde, 1,3-diketone, ethylacetoacetate, and amonium acetate in the presence of cellulose-sulfuric acid as a biosupported solid acid catalyst was developed. The reaction gave the new derivatives of fused 1,4-dihydropyridines in lower reaction times and excellent yields (85–95%.

  3. Investigation on the reactivity of α-azidochalcones with carboxylic acids: Formation of α-amido-1,3-diketones and highly substituted 2-(trifluoromethyloxazoles

    Kandasamy Rajaguru

    2015-10-01

    Full Text Available The reaction of α-azidochalcones with carboxylic acids has been investigated resulting in the formation of α-amido-1,3-diketones under microwave irradiation via in situ formation of 2H-azirine intermediates. An interesting reaction is described wherein, with trifluoroacetic acid at lower temperature, it affords highly substituted 2-(trifluoromethyloxazoles. These flexible transformations proceed under solvent free conditions in good to excellent yields without any catalyst.

  4. Substitution of a single amino acid (aspartic acid for histidine) converts the functional activity of human complement C4B to C4A

    Carroll, M.C.; Fathallah, D.M.; Bergamaschini, L.; Alicot, E.M. (Harvard Medical School, Boston, MA (USA)); Isenman, D.E. (Univ. of Toronto, Ontario (Canada))

    1990-09-01

    The C4B isotype of the fourth component of human complement (C4) displays 3- to 4-fold greater hemolytic activity than does its other isotype C4A. This correlates with differences in their covalent binding efficiencies to erythrocytes coated with antibody and complement C1. C4A binds to a greater extent when C1 is on IgG immune aggregates. The differences in covalent binding properties correlate only with amino acid changes between residues 1101 and 1106 (pro-C4 numbering)-namely, Pro-1101, Cys-1102, Leu-1105, and Asp-1106 in C4A and Leu-1101, Ser-1102, Ile-1105, and His-1106 in C4B, which are located in the C4d region of the {alpha} chain. To more precisely identify the residues that are important for the functional differences, C4A-C4B hybrid proteins were constructed by using recombinant DNA techniques. Comparison of these by hemolytic assay and binding to IgG aggregates showed that the single substitution of aspartic acid for histidine at position 1106 largely accounted for the change in functional activity and nature of the chemical bond formed. Surprisingly, substitution of a neutral residue, alanine, for histidine at position 1106 resulted in an increase in binding to immune aggregates without subsequent reduction in the hemolytic activity. This result strongly suggests that position 1106 is not catalytic as previously proposed but interacts sterically/electrostatically with potential acceptor sites and serves to select binding sites on potential acceptor molecules.

  5. Effects of acute or chronic administration of substituted benzamides in experimental models of depression in rats.

    Drago, F; Arezzi, A; Virzì, A

    2000-12-01

    The effects of substituted benzamides, sulpiride and raclopride on experimental models of depression were studied in male rats after acute or chronic administration in comparison to those of the classical antidepressant, clomipramine. In contrast to clomipramine (50 mg/kg), acute doses of sulpiride or raclopride (1 or 5 mg/kg) failed to change the behavioral response of animals tested in the despair (constrained swim) test or in the model of reserpine-induced changes in the open field behavior. These doses also did not modify the grooming response of rats exposed to a novel environment. Sulpiride or raclopride 10 mg/kg increased the immobility time in the despair test and reduced novelty-induced grooming. The repeated injection for 21 days of sulpiride or raclopride (1 or 5 mg/kg, but not 10 mg/kg) induced a reduction of the immobility period during the constrained swim test similar to that following the chronic treatment with clomipramine 50 mg/kg. This appeared to be a clear-cut reversed dose-response relationship for both substituted benzamides, being the dose potency 1 mg/kg>5 mg/kg>10 mg/kg. Raclopride was more potent than sulpiride in this respect. Furthermore, like clomipramine, sulpiride (1 or 5 mg/kg) and raclopride (1 mg/kg) antagonized reserpine-induced changes in the open field behavior and enhanced novelty-induced grooming. These results indicate that, in contrast to acute injection, repeated administration of small doses of the substituted benzamides, sulpiride or raclopride induce an effect similar to that of the classical antidepressant, clomipramine. The reverse dose-response relationship suggests that these drugs in small doses act on presynaptic dopamine D(2) receptors. This may be consistent with a postsynaptic action of greater doses that exert sedative effects and increase immobility time in the despair test.

  6. Single substitutions to closely related amino acids contribute to the functional diversification of an insect-inducible, positively selected plant cystatin.

    Rasoolizadeh, Asieh; Goulet, Marie-Claire; Sainsbury, Frank; Cloutier, Conrad; Michaud, Dominique

    2016-04-01

    A causal link has been reported between positively selected amino acids in plant cystatins and the inhibitory range of these proteins against insect digestive cysteine (Cys) proteases. Here we assessed the impact of single substitutions to closely related amino acids on the contribution of positive selection to cystatin diversification. Cystatin sequence alignments, while confirming hypervariability, indicated a preference for related amino acids at positively selected sites. For example, the non-polar residues leucine (Leu), isoleucine (Ile) and valine (Val) were shown to predominate at positively selected site 2 in the N-terminal region, unlike selected sites 6 and 10, where polar residues are preferred. The model cystatin SlCYS8 and single variants with Leu, Ile or Val at position 2 were compared with regard to their ability to bind digestive proteases of the coleopteran pest Leptinotarsa decemlineata and to induce compensatory responses in this insect. A functional proteomics procedure to capture target Cys proteases in midgut extracts allowed confirmation of distinct binding profiles for the cystatin variants. A shotgun proteomics procedure to monitor whole Cys protease complements revealed protease family specific compensatory responses in the insect, dependent on the variant ingested. Our data confirm the contribution of closely related amino acids to the functional diversity of positively selected plant cystatins in a broader structure/function context imposing physicochemical constraints to primary structure alterations. They also underline the complexity of protease/inhibitor interactions in plant-insect systems, and the challenges still to be met in order to harness the full potential of ectopically expressed protease inhibitors in crop protection.

  7. L-dehydroascorbic acid can substitute L-ascorbic acid as dietary vitamin C source in guinea pigs

    Frikke-Schmidt, Henriette Rønne; Tveden-Nyborg, Pernille; Lykkesfeldt, Jens

    2016-01-01

    Vitamin C deficiency globally affects several hundred million people and has been associated with increased morbidity and mortality in numerous studies. In this study, bioavailability of the oxidized form of vitamin C (l-dehydroascorbic acid or DHA)-commonly found in vitamin C containing food...... products prone to oxidation-was studied. Our aim was to compare tissue accumulation of vitamin C in guinea pigs receiving different oral doses of either ascorbate or DHA. In all tissues tested (plasma, liver, spleen, lung, adrenal glands, kidney, muscle, heart, and brain), only sporadic differences...... in vitamin C accumulation from ascorbate or DHA were observed except for the lowest dose of DHA (0.25mg/ml in the drinking water), where approximately half of the tissues had slightly yet significantly less vitamin C accumulation than from the ascorbate source. As these results contradicted data from rats...

  8. Lipozyme RM IM-catalyzed acidolysis of Cinnamomum camphora seed oil with oleic acid to produce human milk fat substitutes enriched in medium-chain fatty acids.

    Zou, Xian-Guo; Hu, Jiang-Ning; Zhao, Man-Li; Zhu, Xue-Mei; Li, Hong-Yan; Liu, Xiao-Ru; Liu, Rong; Deng, Ze-Yuan

    2014-10-29

    In the present study, a human milk fat substitute (HMFS) enriched in medium-chain fatty acids (MCFAs) was synthesized through acidolysis reaction from Cinnamomum camphora seed oil (CCSO) with oleic acid in a solvent-free system. A commercial immobilized lipase, Lipozyme RM IM, from Rhizomucor miehei, was facilitated as a biocatalyst. Effects of different reaction conditions, including substrate molar ratio, enzyme concentration, reaction temperature, and reaction time were investigated using response surface methodology (RSM) to obtain the optimal oleic acid incorporation. After optimization, results showed that the maximal incorporation of oleic acid into HMFS was 59.68%. Compared with CCSO, medium-chain fatty acids at the sn-2 position of HMFS accounted for >70%, whereas oleic acid was occupied predominantly at the sn-1,3 position (78.69%). Meanwhile, triacylglycerol (TAG) components of OCO (23.93%), CCO (14.94%), LaCO (13.58%), OLaO (12.66%), and OOO (11.13%) were determined as the major TAG species in HMFS. The final optimal reaction conditions were carried out as follows: substrate molar ratio (oleic acid/CCSO), 5:1; enzyme concentration, 12.5% (w/w total reactants); reaction temperature, 60 °C; and reaction time, 28 h. The reusability of Lipozyme RM IM in the acidolysis reaction was also evaluated, and it was found that it could be reused up to 9 times without significant loss of activities. Urea inclusion method was used to separate and purify the synthetic product. As the ratio of HMFS/urea increased to 1:2, the acid value lowered to the minimum. In a scale-up experiment, the contents of TAG and total tocopherols in HMFS (modified CCSO) were 77.28% and 12.27 mg/100 g, respectively. All of the physicochemical indices of purified product were within food standards. Therefore, such a MCFA-enriched HMFS produced by using the acidolysis method might have potential application in the infant formula industry.

  9. Effect of a bulky lateral substitution by chlorine atom and methoxy group on self-assembling properties of lactic acid derivatives

    Stojanović, Maja, E-mail: maja.stojanovic@df.uns.ac.rs [Department of Physics, Faculty of Sciences, University of Novi Sad, Trg D.Obradovića 4, 21000 Novi Sad (Serbia); Bubnov, Alexej [Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague (Czech Republic); Obadović, Dušanka Ž. [Department of Physics, Faculty of Sciences, University of Novi Sad, Trg D.Obradovića 4, 21000 Novi Sad (Serbia); Hamplová, Věra [Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague (Czech Republic); Cvetinov, Miroslav [Department of Physics, Faculty of Sciences, University of Novi Sad, Trg D.Obradovića 4, 21000 Novi Sad (Serbia); Kašpar, Miroslav [Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Prague (Czech Republic)

    2014-07-01

    Several chiral liquid crystalline materials derived from the lactic acid have been studied with the aim to establish the effect of bulky lateral substituents on their self-assembling properties. A chlorine atom and methoxy group have been used as lateral substituents in ortho position to ether group position on phenyl ring far from the chiral centre. All the studied materials possess tilted ferroelectric smectic C* phase in a broad temperature range. In dependence on the molecular structure namely type of lateral substituent and length of the chiral chain, the cholesteric mesophase, orthogonal paraelectric smectic A* and crystal mesophases have been detected. Lateral chlorine substitution results in decrease of both the clearing point and crystallisation temperature as well as in a distinct increase of spontaneous polarization. Bulky methoxy substitution slightly suppresses the spontaneous polarisation but strongly increases the melting point that results in monotropic peculiarity of the SmC* phase. Mesomorphic, spontaneous, structural and dielectric properties of the substituted compounds were established and compared to those of the non-substituted ones in order to contribute to better understanding of the structure–property relationship for such chiral self-assembling materials. - Highlights: • Chiral liquid crystalline materials derived from the lactic acid have been studied. • Effect of bulky lateral substituents on self-assembling properties has been established. • Bulky methoxy substitution suppresses spontaneous polarisation but increases the melting point. • The compounds might have a strong potential for many advanced electro-optic applications.

  10. Non-Extensive Entropy Econometrics: New Statistical Features of Constant Elasticity of Substitution-Related Models

    Second Bwanakare

    2014-05-01

    Full Text Available Power-law (PL formalism is known to provide an appropriate framework for canonical modeling of nonlinear systems. We estimated three stochastically distinct models of constant elasticity of substitution (CES class functions as non-linear inverse problem and showed that these PL related functions should have a closed form. The first model is related to an aggregator production function, the second to an aggregator utility function (the Armington and the third to an aggregator technical transformation function. A q-generalization of K-L information divergence criterion function with a priori consistency constraints is proposed. Related inferential statistical indices are computed. The approach leads to robust estimation and to new findings about the true stochastic nature of this class of nonlinear—up until now—analytically intractable functions. Outputs from traditional econometric techniques (Shannon entropy, NLLS, GMM, ML are also presented.

  11. Does L to D-amino acid substitution trigger helix→sheet conformations in collagen like peptides adsorbed to surfaces?

    Velmurugan, Punitha; Jonnalagadda, Raghava Rao; Sankaranarayanan, Kamatchi; Dhathathreyan, Aruna

    2015-12-01

    The present work reports on the structural order, self assembling behaviour and the role in adsorption to hydrophilic or hydrophobic solid surfaces of modified sequence from the triple helical peptide model of the collagenase cleavage site in type I collagen (Uniprot accession number P02452 residues from 935 to 970) using (D)Ala and (D)Ile substitutions as given in the models below: Model-1: GSOGADGPAGAOGTOGPQGIAGQRGVV GLOGQRGER. Model-2: GSOGADGP(D)AGAOGTOGPQGIAGQRGVVGLOGQRGER. Model-3: GSOGADGPAGAOGTOGPQG(D)IAGQRGVVGLOGQRGER. Collagenase is an important enzyme that plays an important role in degrading collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism by which this degradation occurs is not completely understood. Our results show that adsorption of the peptides to the solid surfaces, specifically hydrophobic triggers a helix to beta transition with order increasing in peptide models 2 and 3. This restricts the collagenolytic behaviour of collagenase and may find application in design of peptides and peptidomimetics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins.

  12. Special quasirandom structure modeling of fluorite-structured oxide solid solutions with aliovalent cation substitutions

    Wolff-Goodrich, Silas; Hanken, Benjamin E.; Solomon, Jonathan M.; Asta, Mark

    2015-07-01

    The accuracy of the special quasirandom structure (SQS) approach for modeling the structure and energetics of fluorite-structured oxide solid solutions with aliovalent cation substitutions is assessed in an ionic-pair potential study of urania and ceria based systems mixed with trivalent rare-earth ions. Mixing enthalpies for SQS supercells containing 96 and 324 lattice sites were calculated using ionic pair potentials for U0.5La0.5O1.75, U0.5Y0.5O1.75, Ce0.5La0.5O1.75, Ce0.5Y0.5O1.75, and Ce0.5Gd0.5O1.75, which all have stoichiometries of pyrochlores. The SQS results were compared to benchmark values for random substitutional disorder obtained using large supercell models. The calculations show significant improvement of the mixing enthalpy for the larger 324 site SQS, which is attributed to a better description of the structural distortions, as characterized by the radial distribution functions in relaxed systems.

  13. Comparison of Nootropic and Neuroprotective Features of Aryl-Substituted Analogs of Gamma-Aminobutyric Acid.

    Tyurenkov, I N; Borodkina, L E; Bagmetova, V V; Berestovitskaya, V M; Vasil'eva, O S

    2016-02-01

    GABA analogs containing phenyl (phenibut) or para-chlorophenyl (baclofen) substituents demonstrated nootropic activity in a dose of 20 mg/kg: they improved passive avoidance conditioning, decelerated its natural extinction, and exerted antiamnestic effect on the models of amnesia provoked by scopolamine or electroshock. Tolyl-containing GABA analog (tolibut, 20 mg/kg) exhibited antiamnestic activity only on the model of electroshock-induced amnesia. Baclofen and, to a lesser extent, tolibut alleviated seizures provoked by electroshock, i.e. both agents exerted anticonvulsant effect. All examined GABA aryl derivatives demonstrated neuroprotective properties on the maximum electroshock model: they shortened the duration of coma and shortened the period of spontaneous motor activity recovery. In addition, these agents decreased the severity of passive avoidance amnesia and behavioral deficit in the open field test in rats exposed to electroshock. The greatest neuroprotective properties were exhibited by phenyl-containing GABA analog phenibut.

  14. Identification of amino acid substitutions with compensational effects in the attachment protein of canine distemper virus.

    Sattler, Ursula; Khosravi, Mojtaba; Avila, Mislay; Pilo, Paola; Langedijk, Johannes P; Ader-Ebert, Nadine; Alves, Lisa A; Plattet, Philippe; Origgi, Francesco C

    2014-07-01

    The hemagglutinin (H) gene of canine distemper virus (CDV) encodes the receptor-binding protein. This protein, together with the fusion (F) protein, is pivotal for infectivity since it contributes to the fusion of the viral envelope with the host cell membrane. Of the two receptors currently known for CDV (nectin-4 and the signaling lymphocyte activation molecule [SLAM]), SLAM is considered the most relevant for host susceptibility. To investigate how evolution might have impacted the host-CDV interaction, we examined the functional properties of a series of missense single nucleotide polymorphisms (SNPs) naturally accumulating within the H-gene sequences during the transition between two distinct but related strains. The two strains, a wild-type strain and a consensus strain, were part of a single continental outbreak in European wildlife and occurred in distinct geographical areas 2 years apart. The deduced amino acid sequence of the two H genes differed at 5 residues. A panel of mutants carrying all the combinations of the SNPs was obtained by site-directed mutagenesis. The selected mutant, wild type, and consensus H proteins were functionally evaluated according to their surface expression, SLAM binding, fusion protein interaction, and cell fusion efficiencies. The results highlight that the most detrimental functional effects are associated with specific sets of SNPs. Strikingly, an efficient compensational system driven by additional SNPs appears to come into play, virtually neutralizing the negative functional effects. This system seems to contribute to the maintenance of the tightly regulated function of the H-gene-encoded attachment protein. Importance: To investigate how evolution might have impacted the host-canine distemper virus (CDV) interaction, we examined the functional properties of naturally occurring single nucleotide polymorphisms (SNPs) in the hemagglutinin gene of two related but distinct strains of CDV. The hemagglutinin gene encodes the

  15. Optimization of immunoglobulin substitution therapy by a stochastic immune response model.

    Marc Thilo Figge

    Full Text Available BACKGROUND: The immune system is a complex adaptive system of cells and molecules that are interwoven in a highly organized communication network. Primary immune deficiencies are disorders in which essential parts of the immune system are absent or do not function according to plan. X-linked agammaglobulinemia is a B-lymphocyte maturation disorder in which the production of immunoglobulin is prohibited by a genetic defect. Patients have to be put on life-long immunoglobulin substitution therapy in order to prevent recurrent and persistent opportunistic infections. METHODOLOGY: We formulate an immune response model in terms of stochastic differential equations and perform a systematic analysis of empirical therapy protocols that differ in the treatment frequency. The model accounts for the immunoglobulin reduction by natural degradation and by antigenic consumption, as well as for the periodic immunoglobulin replenishment that gives rise to an inhomogeneous distribution of immunoglobulin specificities in the shape space. Results are obtained from computer simulations and from analytical calculations within the framework of the Fokker-Planck formalism, which enables us to derive closed expressions for undetermined model parameters such as the infection clearance rate. CONCLUSIONS: We find that the critical value of the clearance rate, below which a chronic infection develops, is strongly dependent on the strength of fluctuations in the administered immunoglobulin dose per treatment and is an increasing function of the treatment frequency. The comparative analysis of therapy protocols with regard to the treatment frequency yields quantitative predictions of therapeutic relevance, where the choice of the optimal treatment frequency reveals a conflict of competing interests: In order to diminish immunomodulatory effects and to make good economic sense, therapeutic immunoglobulin levels should be kept close to physiological levels, implying high

  16. Parvovirus B19 genotype specific amino acid substitution in NS1 reduces the protein's cytotoxicity in culture.

    Kivovich, Violetta; Gilbert, Leona; Vuento, Matti; Naides, Stanley J

    2010-05-25

    A clinical association between idiopathic liver disease and parvovirus B19 infection has been observed. Fulminant liver failure, not associated with other liver-tropic viruses, has been attributed to B19 in numerous reports, suggesting a possible role for B19 components in the extensive hepatocyte cytotoxicity observed in this condition. A recent report by Abe and colleagues (Int J Med Sci. 2007;4:105-9) demonstrated a link between persistent parvovirus B19 genotype I and III infection and fulminant liver failure. The genetic analysis of isolates obtained from these patients demonstrated a conservation of key amino acids in the nonstructural protein 1 (NS1) of the disease-associated genotypes. In this report we examine a conserved residue identified by Abe and colleagues and show that substitution of isoleucine 181 for methionine, as occurs in B19 genotype II, results in the reduction of B19 NS1-induced cytotoxicity of liver cells. Our results support the hypothesis that in the setting of persistent B19 infection, direct B19 NS1-induced cytotoxicity may play a role in idiopathic fulminant liver failure.

  17. Parvovirus B19 Genotype Specific Amino Acid Substitution in NS1 Reduces the Protein's Cytotoxicity in Culture

    Violetta Kivovich, Leona Gilbert, Matti Vuento, Stanley J. Naides

    2010-01-01

    Full Text Available A clinical association between idiopathic liver disease and parvovirus B19 infection has been observed. Fulminant liver failure, not associated with other liver-tropic viruses, has been attributed to B19 in numerous reports, suggesting a possible role for B19 components in the extensive hepatocyte cytotoxicity observed in this condition. A recent report by Abe and colleagues (Int J Med Sci. 2007;4:105-9 demonstrated a link between persistent parvovirus B19 genotype I and III infection and fulminant liver failure. The genetic analysis of isolates obtained from these patients demonstrated a conservation of key amino acids in the nonstructural protein 1 (NS1 of the disease-associated genotypes. In this report we examine a conserved residue identified by Abe and colleagues and show that substitution of isoleucine 181 for methionine, as occurs in B19 genotype II, results in the reduction of B19 NS1-induced cytotoxicity of liver cells. Our results support the hypothesis that in the setting of persistent B19 infection, direct B19 NS1-induced cytotoxicity may play a role in idiopathic fulminant liver failure.

  18. Antibacterial and biocompatible properties of vancomycin-loaded nano-hydroxyapatite/collagen/poly (lactic acid) bone substitute

    Xiaojie Lian; Huanye Liu; Xiumei Wang; Suju Xu; Fuzhai Cui; Xizhuang Bai

    2013-01-01

    Infected bone defects are normally regarded as contraindications for bone grafting. In the present study, an antibacterial bone graft substitute was synthesized by loading vancomycin (VCM) in our previously developed mineralized collagen based composite, nano-hydroxyapatite/collagen/poly (lactic acid) (nHAC/PLA), aiming to repair large size bone defects and inhibit related infections simultaneously. The VCM/nHAC/PLA showed typical porous structure with a porosity of (80.776.7)%and compressive strength of 1.52 MPa. The delivery of VCM from VCM/nHAC/PLA was detected in vitro for up to 4 weeks. And their antibacterial properties were determined using inhibition ratio assay and inhibition zone assay. Pretty high level of inhibition ratio (more than 99%) was obtained in VCM/nHAC/PLA group. Additionally, a distinct inhibition zone was clearly formed in Staphylococcus aureus bacterium incubation dish with VCM/nHAC/PLA disc for up to 18 days of incubation. Moreover, both of the nHAC/PLA composites with or without VCM exhibited favorable in vitro and in vivo biocompatibilities for rabbit marrow stromal cells (MSCs) adhesion, spreading, proliferation, and triggering no obvious inflammation responses in subcutaneous implantation. Our results suggested that the VCM/nHAC/PLA performed ideal antibacterial property and biocompatibility and has great promise for the treatment of bone defect-related infections in orthopedic surgeries.

  19. The substitution of mineral fertilizers by compost from household waste in Cameroon: economic analysis with a partial equilibrium model.

    Jaza Folefack, Achille Jean

    2009-05-01

    This paper analyses the possibility of substitution between compost and mineral fertilizer in order to assess the impact on the foreign exchange savings in Cameroon of increasing the use of compost. In this regard, a partial equilibrium model was built up and used as a tool for policy simulations. The review of existing literature already suggests that, the compost commercial value i.e. value of substitution (33,740 FCFA tonne(-1)) is higher compared to the compost real price (30,000 FCFA tonne(-1)), proving that it could be profitable to substitute the mineral fertilizer by compost. Further results from the scenarios used in the modelling exercise show that, increasing the compost availability is the most favourable policy for the substitution of mineral fertilizer by compost. This policy helps to save about 18.55% of the annual imported mineral fertilizer quantity and thus to avoid approximately 8.47% of the yearly total import expenditure in Cameroon. The policy of decreasing the transport rate of compost in regions that are far from the city is also favourable to the substitution. Therefore, in order to encourage the substitution of mineral fertilizer by compost, programmes of popularization of compost should be highlighted and be among the top priorities in the agricultural policy of the Cameroon government.

  20. Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids.

    Jiang, Jianfei; Bakan, Ahmet; Kapralov, Alexandr A; Silva, K Ishara; Huang, Zhentai; Amoscato, Andrew A; Peterson, James; Garapati, Venkata Krishna; Saxena, Sunil; Bayir, Hülya; Atkinson, Jeffrey; Bahar, Ivet; Kagan, Valerian E

    2014-06-01

    Mitochondria have emerged as the major regulatory platform responsible for the coordination of numerous metabolic reactions as well as cell death processes, whereby the execution of intrinsic apoptosis includes the production of reactive oxygen species fueling oxidation of cardiolipin (CL) catalyzed by cytochrome (Cyt) c. As this oxidation occurs within the peroxidase complex of Cyt c with CL, the latter represents a promising target for the discovery and design of drugs with antiapoptotic mechanisms of action. In this work, we designed and synthesized a new group of mitochondria-targeted imidazole-substituted analogs of stearic acid TPP-n-ISAs with various positions of the attached imidazole group on the fatty acid (n = 6, 8, 10, 13, and 14). By using a combination of absorption spectroscopy and EPR protocols (continuous wave electron paramagnetic resonance and electron spin echo envelope modulation) we demonstrated that TPP-n-ISAs indeed were able to potently suppress CL-induced structural rearrangements in Cyt c, paving the way to its peroxidase competence. TPP-n-ISA analogs preserved the low-spin hexa-coordinated heme-iron state in Cyt c/CL complexes whereby TPP-6-ISA displayed a significantly more effective preservation pattern than TPP-14-ISA. Elucidation of these intermolecular stabilization mechanisms of Cyt c identified TPP-6-ISA as an effective inhibitor of the peroxidase function of Cyt c/CL complexes with a significant antiapoptotic potential realized in mouse embryonic cells exposed to ionizing irradiation. These experimental findings were detailed and supported by all-atom molecular dynamics simulations. Based on the experimental data and computation predictions, we identified TPP-6-ISA as a candidate drug with optimized antiapoptotic potency.

  1. Chelation in Metal Intoxication XLVI:Synthesis of Some α-Mercapto-β-Substituted Aryl Acrylic Acids and Their In vitro Cadmium Chelating Ability

    MADHUMITA CHATTERJEE; VINOD K. DWIVEDI; KIRTI KHANDEKAR; SUSHIL K. TANDON

    2004-01-01

    Objective To synthesize some new α-mercapto-β-substituted aryl acrylic acids, characterize them and investigate their in vitro cadmium chelating ability. Methods Six α-mercapto-β-substituted aryl acrylic acids were prepared by the alkaline hydrolysis of 5-(aryl methylene)rhodanines, obtained from the condensation of substituted aldehydes and rhodanine following the reported procedure. The new compounds were characterized by elemental analysis, infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy. The liver and kidney from cadmium chloride pre-administered rats were homogenized and their nuclear mitochondrial fraction (NMF) and supernatant cytosol fraction (SCF) were separated. A measured volume of each fraction was dialyzed separately using "dialysis sack" against buffered-KCl medium containing a compound in the final concentration of 1×10-3 mol/L for 3 h at 37℃C. The whole content of "sack" was subjected to cadmiumestimation following digestion with conc. Nitric acid was detected using flame atomic absorption spectrometer. Results The in vitro screening showed that α-mercapto-β-(p-methoxyphenyl)acrylic acid (compound 2) and α-mercapto-β-(m-methoxy, p-hydroxyphenyl) acrylic acid (compound 4) were more effective than α-mercapto-β-thienyl acrylic acid (compound 1) and α-mercapto-β-(p-dimethylaminophenyl) acrylic acid (compound 3) in mobilizing cadmium as their dialyzable chelates. The presence of a methoxy group on the phenyl moiety (compounds 2 and 4) increases the metal chelating ability of mercapto acrylic acids. Conclusions Compounds 2 and 4 seem to have accessibility to the cellular system and capability of chelating-out the intracellularly bound cadmium.

  2. A Single Amino Acid Substitution Converts Benzophenone Synthase into Phenylpyrone Synthase*

    Klundt, Tim; Bocola, Marco; Lütge, Maren; Beuerle, Till; Liu, Benye; Beerhues, Ludger

    2009-01-01

    Benzophenone metabolism provides a number of plant natural products with fascinating chemical structures and intriguing pharmacological activities. Formation of the carbon skeleton of benzophenone derivatives from benzoyl-CoA and three molecules of malonyl-CoA is catalyzed by benzophenone synthase (BPS), a member of the superfamily of type III polyketide synthases. A point mutation in the active site cavity (T135L) transformed BPS into a functional phenylpyrone synthase (PPS). The dramatic change in both substrate and product specificities of BPS was rationalized by homology modeling. The mutation may open a new pocket that accommodates the phenyl moiety of the triketide intermediate but limits polyketide elongation to two reactions, resulting in phenylpyrone formation. 3-Hydroxybenzoyl-CoA is the second best starter molecule for BPS but a poor substrate for PPS. The aryl moiety of the triketide intermediate may be trapped in the new pocket by hydrogen bond formation with the backbone, thereby acting as an inhibitor. PPS is a promising biotechnological tool for manipulating benzoate-primed biosynthetic pathways to produce novel compounds. PMID:19710020

  3. Whole body acid-base modeling revisited.

    Ring, Troels; Nielsen, Søren

    2017-04-01

    The textbook account of whole body acid-base balance in terms of endogenous acid production, renal net acid excretion, and gastrointestinal alkali absorption, which is the only comprehensive model around, has never been applied in clinical practice or been formally validated. To improve understanding of acid-base modeling, we managed to write up this conventional model as an expression solely on urine chemistry. Renal net acid excretion and endogenous acid production were already formulated in terms of urine chemistry, and we could from the literature also see gastrointestinal alkali absorption in terms of urine excretions. With a few assumptions it was possible to see that this expression of net acid balance was arithmetically identical to minus urine charge, whereby under the development of acidosis, urine was predicted to acquire a net negative charge. The literature already mentions unexplained negative urine charges so we scrutinized a series of seminal papers and confirmed empirically the theoretical prediction that observed urine charge did acquire negative charge as acidosis developed. Hence, we can conclude that the conventional model is problematic since it predicts what is physiologically impossible. Therefore, we need a new model for whole body acid-base balance, which does not have impossible implications. Furthermore, new experimental studies are needed to account for charge imbalance in urine under development of acidosis.

  4. Effects of the substitution of amino acid residues, through chemical synthesis, on the conformation and activity of antimicrobial peptides

    Regina C. Adão

    2012-06-01

    Full Text Available Antimicrobial peptides make up an assorted group of molecules which contain from 12 to 50 amino acid residues and which may be produced by microorganisms, plants and animals. From the discovery that these biomolecules are lethal to bacteria, inhibiting the pathogenic organism’s growth, and are also related to innate and adapted defense mechanisms, the investigation of such molecules came to be an emergent research field, in which more than 1800 antimicrobial peptides have so far been discovered throughout the last three decades. These molecules are potential representatives of a new generation of antibiotic agents and the main motivation for such use is their activity against a wide variety of pathogens, including Gram-positive and Gram-negative bacteria as well as fungi and viruses. An important class of comprising some of these peptides may be found in anurans, from which it has been isolated, a considerable number of antimicrobial peptides with diverse sequences and structures, including linear and dimeric ones. In this work monomeric chains (CH1 e CH2 of the heterodimeric antimicrobial peptide distinctin (isolated in 1999 from Phyllomedusa distincta anurans, as well as its mutated monomers (CH1-S and CH2-S and the heterodimer itself were synthesized. The distinctin is the peptide with two chains of different sequences (Table 1 bound each other by disulfide bond from the cystein residues constituting the heterodimer. To investigate the effects on the biological activity by amino acids substitution at normal distinctin CH1 and CH2 chains, both were synthesized as well as their similar chains (CH1-S and CH2-S in which the cystein (Fig.1 a residues of each chain were changed by serin residues (Fig. 1 b. The new chains were named mutants. The synthesis was carried out in solid phase, using Fmoc strategy. The heterodimer distinctin was obtained from CH1 and CH2 chains coupling through cystein residues air oxidation. The results from HPLC

  5. An equilibrium model for ligand-modified micellar-enhanced ultrafiltration. Selective separation of metal ions using iminoacetic substituted polyamines and a theoretical model for the titration behavior of polyamines

    Dharmawardana, Udeni Rajaratna [Univ. of Oklahoma, Norman, OK (United States)

    1992-01-01

    This thesis consists of three chapters. Chapter 1, An equilibrium model for ligand-modified micellar-enhanced ultrafiltration, describes a theoretical model and experimental investigations which used the semi-equilibrium-dialysis method with N-n-dodecyl iminodiacetic acid as the ligand. In Chapter 2, Selective separation of metal ions using iminoacetic substituted polyamines, polyamines with a substituted ligand group are synthesized and used in investigating selective separation of copper ions from aqueous solution. In Chapter 3, A theoretical model for the titration behavior of polyamines, a novel approach to explain the titration behavior of polymeric amines based on the binding behavior of counterions is described. The application of this study is to the investigation of inexpensive and efficient methods of industrial waste water treatment.

  6. Efficient continuous-flow synthesis of novel 1,2,3-triazole-substituted β-aminocyclohexanecarboxylic acid derivatives with gram-scale production

    Sándor B. Ötvös

    2013-07-01

    Full Text Available The preparation of novel multi-substituted 1,2,3-triazole-modified β-aminocyclohexanecarboxylic acid derivatives in a simple and efficient continuous-flow procedure is reported. The 1,3-dipolar cycloaddition reactions were performed with copper powder as a readily accessible Cu(I source. Initially, high reaction rates were achieved under high-pressure/high-temperature conditions. Subsequently, the reaction temperature was lowered to room temperature by the joint use of both basic and acidic additives to improve the safety of the synthesis, as azides were to be handled as unstable reactants. Scale-up experiments were also performed, which led to the achievement of gram-scale production in a safe and straightforward way. The obtained 1,2,3-triazole-substituted β-aminocyclohexanecarboxylates can be regarded as interesting precursors for drugs with possible biological effects.

  7. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

    Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

    2014-09-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential

  8. Hydroxyapatite-calcium sulfate-hyaluronic acid composite encapsulated with collagenase as bone substitute for alveolar bone regeneration.

    Subramaniam, Sadhasivam; Fang, Yen-Hsin; Sivasubramanian, Savitha; Lin, Feng-Huei; Lin, Chun-pin

    2016-01-01

    Periodontitis is a very severe inflammatory condition of the periodontium that progressively damages the soft tissue and destroys the alveolar bone that supports the teeth. The bone loss is naturally irreversible because of limited reparability of the teeth. Advancement in tissue engineering provides an effective regeneration of osseous defects with suitable dental implants or tissue-engineered constructs. This study reports a hydroxyapatite, calcium sulfate hemihydrate and hyaluronic acid laden collagenase (HAP/CS/HA-Col) as a bone substitute for the alveolar bone regeneration. The composite material was mechanically tested and the biocompatibility was evaluated by WST-1 assay. The in vivo bone formation was assessed in rat with alveolar bone defects and the bone augmentation by the HAP/CS/HA-Col composite was confirmed by micro-CT images and histological examination. The mechanical strength of 6.69 MPa with excellent biocompatibility was obtained for the HAP/CS/HA-Col composite. The collagenase release profile had facilitated the acceleration of bone remodeling process and it was confirmed by the findings of micro-CT and H&E staining. The bone defects implanted with HAP/CS/HA composite containing 2 mg/mL type I collagenase have shown improved new bone formation with matured bone morphology in comparison with the HAP/CS/HA composite that lacks the collagenase and the porous hydroxyapatite (p-HAP) granules. The said findings demonstrated that the collagenase inclusion in HAP/CS/HA composite is a feasible approach for the alveolar bone regeneration and the same design can also be applied to other defective tissues.

  9. Brøsted Acidic Ionic Liquid ([Bmim]Hso4 Promoted Cyclocodensation Reaction: Synthesis of 3,4,5-Substituted Furan-2(5h-Ones

    Sajjad Salahi

    2015-12-01

    Full Text Available 1-Butyl-3-methylimidazolium hydrogen sulfate [bmim]HSO4: an acidic ionic liquid was used as a catalyst for the synthesis of heterocyclic compounds 3,4,5-substituted furan-2(5H-ones from aniline derivatives, dialkyl acetylenedicarboxylates and aromatic aldehydes at 75 °C. Solvent-free conditions, shorter reaction time, and good yields (71-94% are some of advantages.

  10. The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP

    Buhrke, David; Velazquez Escobar, Francisco; Sauthof, Luisa; Wilkening, Svea; Herder, Nico; Tavraz, Neslihan N.; Willoweit, Mario; Keidel, Anke; Utesch, Tillmann; Mroginski, Maria-Andrea; Schmitt, Franz-Josef; Hildebrandt, Peter; Friedrich, Thomas

    2016-01-01

    Bacteriophytochromes are promising tools for tissue microscopy and imaging due to their fluorescence in the near-infrared region. These applications require optimization of the originally low fluorescence quantum yields via genetic engineering. Factors that favour fluorescence over other non-radiative excited state decay channels are yet poorly understood. In this work we employed resonance Raman and fluorescence spectroscopy to analyse the consequences of multiple amino acid substitutions on fluorescence of the iRFP713 benchmark protein. Two groups of mutations distinguishing iRFP from its precursor, the PAS-GAF domain of the bacteriophytochrome P2 from Rhodopseudomonas palustris, have qualitatively different effects on the biliverdin cofactor, which exists in a fluorescent (state II) and a non-fluorescent conformer (state I). Substitution of three critical amino acids in the chromophore binding pocket increases the intrinsic fluorescence quantum yield of state II from 1.7 to 5.0% due to slight structural changes of the tetrapyrrole chromophore. Whereas these changes are accompanied by an enrichment of state II from ~40 to ~50%, a major shift to ~88% is achieved by remote amino acid substitutions. Additionally, an increase of the intrinsic fluorescence quantum yield of this conformer by ~34% is achieved. The present results have important implications for future design strategies of biofluorophores. PMID:27329837

  11. Effects of Single Amino Acid Substitution on the Biophysical Properties and Biological Activities of an Amphipathic α-Helical Antibacterial Peptide Against Gram-Negative Bacteria

    Juanjuan Tan

    2014-07-01

    Full Text Available An antimicrobial peptide, known as V13K, was utilized as the framework to study the effects of charge, hydrophobicity and helicity on the biophysical properties and biological activities of α-helical peptides. Six amino acids (Lys, Glu, Gly, Ser, Ala, and Leu were individually used to substitute the original hydrophobic valine at the selected sixteenth location on the non-polar face of V13K. The results showed that the single amino acid substitutions changed the hydrophobicity of peptide analogs as monitored by RP-HPLC, but did not cause significant changes on peptide secondary structures both in a benign buffer and in a hydrophobic environment. The biological activities of the analogs exhibited a hydrophobicity-dependent behavior. The mechanism of peptide interaction with the outer membrane and cytoplasmic membrane of Gram-negative bacteria was investigated. We demonstrated that this single amino acid substitution method has valuable potential for the rational design of antimicrobial peptides with enhanced activities.

  12. The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP.

    Buhrke, David; Velazquez Escobar, Francisco; Sauthof, Luisa; Wilkening, Svea; Herder, Nico; Tavraz, Neslihan N; Willoweit, Mario; Keidel, Anke; Utesch, Tillmann; Mroginski, Maria-Andrea; Schmitt, Franz-Josef; Hildebrandt, Peter; Friedrich, Thomas

    2016-06-22

    Bacteriophytochromes are promising tools for tissue microscopy and imaging due to their fluorescence in the near-infrared region. These applications require optimization of the originally low fluorescence quantum yields via genetic engineering. Factors that favour fluorescence over other non-radiative excited state decay channels are yet poorly understood. In this work we employed resonance Raman and fluorescence spectroscopy to analyse the consequences of multiple amino acid substitutions on fluorescence of the iRFP713 benchmark protein. Two groups of mutations distinguishing iRFP from its precursor, the PAS-GAF domain of the bacteriophytochrome P2 from Rhodopseudomonas palustris, have qualitatively different effects on the biliverdin cofactor, which exists in a fluorescent (state II) and a non-fluorescent conformer (state I). Substitution of three critical amino acids in the chromophore binding pocket increases the intrinsic fluorescence quantum yield of state II from 1.7 to 5.0% due to slight structural changes of the tetrapyrrole chromophore. Whereas these changes are accompanied by an enrichment of state II from ~40 to ~50%, a major shift to ~88% is achieved by remote amino acid substitutions. Additionally, an increase of the intrinsic fluorescence quantum yield of this conformer by ~34% is achieved. The present results have important implications for future design strategies of biofluorophores.

  13. Amino acid substitutions in the FXYD motif enhance phospholemman-induced modulation of cardiac L-type calcium channels.

    Guo, Kai; Wang, Xianming; Gao, Guofeng; Huang, Congxin; Elmslie, Keith S; Peterson, Blaise Z

    2010-11-01

    We have found that phospholemman (PLM) associates with and modulates the gating of cardiac L-type calcium channels (Wang et al., Biophys J 98: 1149-1159, 2010). The short 17 amino acid extracellular NH(2)-terminal domain of PLM contains a highly conserved PFTYD sequence that defines it as a member of the FXYD family of ion transport regulators. Although we have learned a great deal about PLM-dependent changes in calcium channel gating, little is known regarding the molecular mechanisms underlying the observed changes. Therefore, we investigated the role of the PFTYD segment in the modulation of cardiac calcium channels by individually replacing Pro-8, Phe-9, Thr-10, Tyr-11, and Asp-12 with alanine (P8A, F9A, T10A, Y11A, D12A). In addition, Asp-12 was changed to lysine (D12K) and cysteine (D12C). As expected, wild-type PLM significantly slows channel activation and deactivation and enhances voltage-dependent inactivation (VDI). We were surprised to find that amino acid substitutions at Thr-10 and Asp-12 significantly enhanced the ability of PLM to modulate Ca(V)1.2 gating. T10A exhibited a twofold enhancement of PLM-induced slowing of activation, whereas D12K and D12C dramatically enhanced PLM-induced increase of VDI. The PLM-induced slowing of channel closing was abrogated by D12A and D12C, whereas D12K and T10A failed to impact this effect. These studies demonstrate that the PFXYD motif is not necessary for the association of PLM with Ca(V)1.2. Instead, since altering the chemical and/or physical properties of the PFXYD segment alters the relative magnitudes of opposing PLM-induced effects on Ca(V)1.2 channel gating, PLM appears to play an important role in fine tuning the gating kinetics of cardiac calcium channels and likely plays an important role in shaping the cardiac action potential and regulating Ca(2+) dynamics in the heart.

  14. Synthesis and Application of Acid Dyes Based on 3-(4-Aminophenyl-5-benzylidene-2-substituted phenyl-3, 5-dihydroimidazol-4-one

    Devang N. Wadia

    2008-01-01

    Full Text Available A series of eight novel heterocyclic based monoazo acid dyes were synthesized using various substituted imidazol-4-one as diazo component and coupled with various amino-napthol sulphonic acids. The resultant dyes were characterized using standard spectroscopic methods and then dyeing performance on wool fabric was assessed. Final results concluded that exhaustion (%E of the dyes on wool fibers increased with decreasing pH of application and that fixation (%F of the dyes on wool fibers increased with increasing pH of application and the highest total fixation efficiency was achieved at pH 5. Wash and light fastness properties of prepared dyes showed encouraging results.

  15. Asymmetric synthesis of highly substituted β-lactones through oxidative carbene catalysis with LiCl as cooperative Lewis acid.

    Bera, Srikrishna; Samanta, Ramesh C; Daniliuc, Constantin G; Studer, Armido

    2014-09-01

    The reaction of enals with β-diketones, β-ketoesters, and malonates bearing a β-oxyalkyl substituent at the α-position by oxidative NHC catalysis to provide highly substituted β-lactones is described. Reactions occur with excellent diastereo- and enantioselectivity. The organo cascade comprises two CC bond formations and one CO bond formation. Up to four contiguous stereogenic centers including two fully substituted stereocenters are formed in the cascade.

  16. Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model.

    Sharma, Ity; Kaminski, George A

    2012-11-15

    We have computed pK(a) values for 11 substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides, and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pK(a) values of propanoic and butanoic acids within about 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it uses either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of using the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent.

  17. Synthesis, pharmacological study and modeling of 7-methoxyindazole and related substituted indazoles as neuronal nitric oxide synthase inhibitors.

    Collot, Valérie; Sopkova-de Oliveira Santos, Jana; Schumann-Bard, Pascale; Colloc'h, Nathalie; Mackenzie, Eric T; Rault, Sylvain

    2003-04-01

    The synthesis, pharmacological evaluation and modelisation of 7-methoxyindazole (7-MI) and related alkoxyindazoles as novel inhibitors of neuronal nitric oxide synthase are presented. 7-MI remains the most active compound of this series in an in vitro enzymatic assay of neuronal nitric oxide synthase activity. Modeling studies of the interaction of 7-substituted indazole derivatives complexed with nNOS and the relationship with their respective biological activities suggest that a bulky substitution on position-7 is responsible for a steric hindrance effect which does not allow these compounds to interact with nNOS in the same way as 7-NI and 7-MI.

  18. Cotton chromosome substitution lines crossed with cultivars: genetic model evaluation and seed trait analyses.

    Wu, Jixiang; McCarty, Jack C; Jenkins, Johnie N

    2010-05-01

    Seed from upland cotton, Gossypium hirsutum L., provides a desirable and important nutrition profile. In this study, several seed traits (protein content, oil content, seed hull fiber content, seed index, seed volume, embryo percentage) for F(3) hybrids of 13 cotton chromosome substitution lines crossed with five elite cultivars over four environments were evaluated. Oil and protein were expressed both as percentage of total seed weight and as an index which is the grams of product/100 seeds. An additive and dominance (AD) genetic model with cytoplasmic effects was designed, assessed by simulations, and employed to analyze these seed traits. Simulated results showed that this model was sufficient for analyzing the data structure with F(3) and parents in multiple environments without replications. Significant cytoplasmic effects were detected for seed oil content, oil index, seed index, seed volume, and seed embryo percentage. Additive effects were significant for protein content, fiber content, protein index, oil index, fiber index, seed index, seed volume, and embryo percentage. Dominance effects were significant for oil content, oil index, seed index, and seed volume. Cytoplasmic and additive effects for parents and dominance effects in homozygous and heterozygous forms were predicted. Favorable genetic effects were predicted in this study and the results provided evidence that these seed traits can be genetically improved. In addition, chromosome associations with AD effects were detected and discussed in this study.

  19. Canine distemper virus neutralization activity is low in human serum and it is sensitive to an amino acid substitution in the hemagglutinin protein

    Zhang, Xinsheng, E-mail: xzhang@iavi.org [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Molecular and Cellular Biology Program, State University of New York, Brooklyn, NY (United States); Wallace, Olivia L.; Domi, Arban; Wright, Kevin J.; Driscoll, Jonathan [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Anzala, Omu [Kenya AIDS Vaccine Initiative (KAVI)-Institute of Clinical Research, Nairobi (Kenya); Sanders, Eduard J. [Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya & Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington (United Kingdom); Kamali, Anatoli [MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka and Entebbe (Uganda); Karita, Etienne [Projet San Francisco, Kigali (Rwanda); Allen, Susan [Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States); Fast, Pat [Department of Medical Affairs, International AIDS Vaccine Initiative, NY, NY (United States); Gilmour, Jill [Human Immunology Laboratory, International AIDS Vaccine Initiative, London (United Kingdom); Price, Matt A. [Department of Medical Affairs, International AIDS Vaccine Initiative, NY, NY (United States); Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA (United States); Parks, Christopher L. [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Molecular and Cellular Biology Program, State University of New York, Brooklyn, NY (United States)

    2015-08-15

    Serum was analyzed from 146 healthy adult volunteers in eastern Africa to evaluate measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb) prevalence and potency. MV plaque reduction neutralization test (PRNT) results indicated that all sera were positive for MV nAbs. Furthermore, the 50% neutralizing dose (ND50) for the majority of sera corresponded to antibody titers induced by MV vaccination. CDV nAbs titers were low and generally were detected in sera with high MV nAb titers. A mutant CDV was generated that was less sensitive to neutralization by human serum. The mutant virus genome had 10 nucleotide substitutions, which coded for single amino acid substitutions in the fusion (F) and hemagglutinin (H) glycoproteins and two substitutions in the large polymerase (L) protein. The H substitution occurred in a conserved region involved in receptor interactions among morbilliviruses, implying that this region is a target for cross-reactive neutralizing antibodies. - Highlights: • Screened 146 serum samples for measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb). • MV nAb is prevalent in the sera. • CDV neutralizing activity is generally low or absent and when detected it is present in sera with high MV nAb titers. • A neutralization-resistant CDV mutant was isolated using human serum selection. • A mutation was identified in the receptor-binding region of CDV hemagglutinin protein that confers the neutralization resistance.

  20. Determination of small halogenated carboxylic acid residues in drug substances by high performance liquid chromatography-diode array detection following derivatization with nitro-substituted phenylhydrazines.

    Hou, Desheng; Fan, Jingjing; Han, Lingfei; Ruan, Xiaoling; Feng, Feng; Liu, Wenyuan; Zheng, Feng

    2016-03-18

    A method for the determination of small halogenated carboxylic acid (HCA) residues in drug substances is urgently needed because of the potential of HCAs for genotoxicity and carcinogenicity in humans. We have now developed a simple method, involving derivatization followed by high performance liquid chromatography-diode array detection (HPLC-DAD), for the determination of six likely residual HCAs (monochloroacetic acid, monobromoacetic acid, dichloroacetic acid, 2-chloropropionic acid, 2-bromopropionic acid and 3-chloropropionic acid) in drug substances. Different nitro-substituted phenylhydrazines (NPHs) derivatization reagents were systematically compared and evaluated. 2-Nitrophenylhydrazine hydrochloride (2-NPH·HCl) was selected as the most suitable choice since its derivatives absorb strongly at 392 nm, a region of the spectrum where most drug substances and impurities absorb very weakly. During the derivatization process, the commonly used catalyst, pyridine, caused rapid dechlorination or chlorine substitution of α-halogenated derivatives. To avoid these unwanted side reactions, a reliable derivatization method that did not use pyridine was developed. Reaction with 2-NPH·HCl using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride as coupling agent in acetonitrile-water (70:30) at room temperature for 2h gave complete reaction and avoided degradation products. The derivatives were analyzed, without any pretreatment, using gradient HPLC with detection in the near visible region. Organic acids commonly found in drug substances and other impurities did not interfere with the analysis. Good linearity (r>0.999) and low limits of quantitation (0.05-0.12 μg mL(-1)) were obtained. The mean recoveries were in the range of 80-115% with RSD <5.81% except for 3-CPA in ibuprofen which was 78.5%. The intra- and inter-day precisions were expressed as RSD <1.98% and <4.39%, respectively. Finally, the proposed method was successfully used for the residue

  1. Tissue engineering for total meniscal substitution : Animal study in sheep model

    Kon, Elizaveta; Chiari, Catharina; Marcacci, Maurilio; Delcogliano, Marco; Donald M Salter; Martin, Ivan; Ambrosio, Luigi; Fini, Milena; Tschon, Matilde; Tognana, Enrico; Plasenzotti, Roberto; Nehrer, Stefan

    2008-01-01

    Objective: The aim of the study was to investigate the use of a novel hyaluronic acid/polycaprolactone material for meniscal tissue engineering and to evaluate the tissue regeneration after the augmentation of the implant with expanded autologous chondrocytes. Two different surgical implantation techniques in a sheep model were evaluated. Methods: Twenty-four skeletally mature sheep were treated with total medial meniscus replacements, while two meniscectomies served as empty controls. The an...

  2. Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

    Leenheer, J.A.; Brown, G.K.; Cabaniss, S.E. [Geological Survey, Denver, CO (United States); MacCarthy, P. [Colorado School of Mines, Golden, CO (United States). Dept. of Chemistry

    1998-08-15

    Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca{sup 2+}, Cd{sup 2+}, Cu{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca{sup 2+} ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The metal binding fraction was characterized by quantitative {sup 13}C NMR, {sup 1}H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca{sup 2+} binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.

  3. Molybdenum (VI) binded to humic and nitrohumic acid models in aqueous solutions salicylic, 3-nitrosalicylic, 5-nitrosalicylic and 3,5 dinitrosalicylic acids, Part 2

    Merce, Ana Lucia R.; Lopes, Priscilla P.; Mangricha, Antonio S. [Parana Univ., Curitiba, PR (Brazil). Dept. de Quimica]. E-mail: anamerce@ufpr.br; Levy, Noel M. [Companhia Paranaense de Energia (COPEL), Curitiba, PR (Brazil)

    2006-05-15

    In this work electrochemical and Ultraviolet-Visible studies were performed in solutions of salicylic acid models of humic and nitrohumic acids, a laboratory artifact, and molybdenum in order to determine the affinity of these models towards the metal ion. Molybdenum, which plays a very important role in the soil chemistry, and together with humic substances, impart fertility to soil and water and is a key element in the activity of nitrogenase. The obtained results showed that at least one complexed species is present at the pH range of 6.3 to 8.0, even for the less basic chosen models, the nitrosalicylic acids. Previous study showed that phthalic and nitrophthalic, also humic and nitrohumic acids model compounds, presented complexed species with molybdenum only till pH 6.5. The calculated formation constants showed that the substitution of the nitro group in the orto position was less favoured than in the para substitution, probably due to a steric hindrance in the former, which was clearly seen in the double substituted salicylic nitro derivative. The cyclic voltammetry as well as the Ultraviolet-Visible obtained spectra were able to show that the chemistry of molybdenum in aqueous solutions as the pH is increased is very complex, and the molybdate stops acting as an anion only after pH around 4, when it finally becomes a cation MoO{sub 2}{sup 2+} (M). (author)

  4. Modelling and simulation of photocatalytic oxidation mechanism of chlorohalogenated substituted phenols in batch systems: Langmuir-Hinshelwood approach.

    Khuzwayo, Z; Chirwa, E M N

    2015-12-30

    This study investigated, modelled and simulated the influence of multi-chlorohalogenation in heterogeneous photocatalytic degradation of substituted phenols (pentachlorophenol (PCP), trichlorophenol (TCP), dichlorophenol (DCP), and monochlorophenol (CP)). The Langmuir-Hinshelwood approach was applied to determine oxidation kinetics. Aquasim 2.0 computational software was used to model, simulate and estimate model parameters of the different chlorophenols. Chemical adsorption equilibrium isotherms for the four chlorophenols and phenol were studied and modelled for adsorption onto titanium dioxide (TiO2) semiconductor catalyst. Langmuir adsorption parameters were determined and used to calculate adsorption constant and maximum adsorption capacity. The adsorption of chloride phenolics onto titanium dioxide catalyst increased in the order of 4 - CP Photocatalytic studies analysed the efficiency of oxidation and found improved degradation with higher chloride substituted phenolics in the order of PCP > TCP > DCP ≥ 4 - CP. Photocatalytic parameters were calculated and estimated along with sensitivity and uncertainty analyses.

  5. Substitution patterns in aromatic rings by increment analysis. Model development and application to natural organic matter.

    Perdue, E M; Hertkorn, N; Kettrup, A

    2007-02-01

    The aromatic region of two-dimensional heteronuclear 1H, 13C NMR spectra of natural organic matter and related materials (e.g., 1H and 13C chemical shifts ranging from approximately 5 to 10 and 80 to 140 ppm, respectively) is highly complex and difficult to interpret using conventional approaches. In principle, this region of the NMR spectrum should be amenable to detailed analysis, because the effects of many common substituents on the chemical shifts of aromatic carbon and hydrogen are well documented. This paper describes the development of a model for prediction of substitution patterns in aromatic rings by increment analysis (SPARIA). In the forward mode, SPARIA is used to predict the chemical shifts of 1H and 13C on aromatic moieties containing every possible combination of eight common substituents that are likely to be representative of substituents on aromatic moieties in natural organic matter. The accuracy of SPARIA in the forward mode is evaluated for 29 aromatic compounds (100 peaks) by comparison of predicted chemical shifts for 1H and 13C with experimental values and with predictions of commercially available software for prediction of NMR spectra. The most important development in this paper is the inverse mode that is built into SPARIA. Given chemical shifts for 1H and 13C (such as may be obtained from a two-dimensional, heteronuclear NMR spectrum), the inverse mode of SPARIA calculates all possible combinations of the eight selected substituents that yield chemical shifts within a specified window of chemical shift for both 1H and 13C. Both the distribution of possible substitution patterns and simple descriptive statistics of the distribution are thus obtained. The inverse mode of SPARIA has been tested on the 29 aromatic compounds (100 peaks) that were used to evaluate its forward mode, and the dependence of the inverse process on the size of the chemical shift window has been evaluated. Finally, the inverse mode of SPARIA has been applied to

  6. Transformation of Tri-Titanium(IV-Substituted α-Keggin Polyoxometalate (POM into Tetra-Titanium(IV-Substituted POMs : Reaction Products of Titanium(IV Sulfate with the Dimeric Keggin POM Precursor under Acidic Conditions

    Kenji Nomiya

    2010-01-01

    Full Text Available Reaction products of titanium(IV sulfate in HCl-acidic aqueous solution with the dimeric species linked through three intermolecular Ti-O-Ti bonds of the two tri-titanium(IV-substituted α-Keggin polyoxometalate (POM subunits are described. Two novel titanium(IV-containing α-Keggin POMs were obtained under different conditions. One product was a dimeric species through two intermolecular Ti-O-Ti bonds of the two tetra-titanium(IV-substituted α-Keggin POM subunits, i.e., [[{Ti(H2O3}2(μ-O](α-PW9Ti2O38]26- (1. The other product was a monomeric α-Keggin species containing the tetra-titanium(IV oxide cluster and two coordinated sulfate ions, i.e., [{Ti4(μ-O3(SO42(H2O8}(α-PW9O34]3- (2. Molecular structures of 1 and 2 were also discussed based on host (lacunary site-guest (titanium atom chemistry.

  7. Mefenamic Acid Induced Nephrotoxicity: An Animal Model

    Muhammad Nazrul Somchit

    2014-12-01

    Full Text Available Purpose: Nonsteroidal anti-inflammatory drugs (NSAIDs are used for the treatment of many joint disorders, inflammation and to control pain. Numerous reports have indicated that NSAIDs are capable of producing nephrotoxicity in human. Therefore, the objective of this study was to evaluate mefenamic acid, a NSAID nephrotoxicity in an animal model. Methods: Mice were dosed intraperitoneally with mefenamic acid either as a single dose (100 or 200 mg/kg in 10% Dimethyl sulfoxide/Palm oil or as single daily doses for 14 days (50 or 100 mg/kg in 10% Dimethyl sulfoxide/Palm oil per day. Venous blood samples from mice during the dosing period were taken prior to and 14 days post-dosing from cardiac puncture into heparinized vials. Plasma blood urea nitrogen (BUN and creatinine activities were measured. Results: Single dose of mefenamic acid induced mild alteration of kidney histology mainly mild glomerular necrosis and tubular atrophy. Interestingly, chronic doses induced a dose dependent glomerular necrosis, massive degeneration, inflammation and tubular atrophy. Plasma blood urea nitrogen was statistically elevated in mice treated with mefenamic acid for 14 days similar to plasma creatinine. Conclusion: Results from this study suggest that mefenamic acid as with other NSAIDs capable of producing nephrotoxicity. Therefore, the study of the exact mechanism of mefenamic acid induced severe nephrotoxicity can be done in this animal model.

  8. Activity of ceftazidime/avibactam against isogenic strains of Escherichia coli containing KPC and SHV β-lactamases with single amino acid substitutions in the Ω-loop

    Winkler, Marisa L.; Papp-Wallace, Krisztina M.; Bonomo, Robert A.

    2015-01-01

    Objectives The objective of this study was to explore the activity of ceftazidime and ceftazidime/avibactam against a collection of isogenic strains of Escherichia coli DH10B possessing SHV and KPC β-lactamases containing single amino acid substitutions in the Ω-loop (residues 164–179). Methods Ceftazidime and ceftazidime/avibactam MICs were determined by the agar dilution method for a panel of isogenic E. coli strains expressing SHV-1 and KPC-2 with amino acid substitutions at positions 164, 167, 169 or 179. Two KPC-2 β-lactamase variants that possessed elevated MICs of ceftazidime/avibactam were selected for further biochemical analyses. Results Avibactam restored susceptibility to ceftazidime for all Ω-loop variants of SHV-1 with MICs 8 mg/L. β-Lactamase kinetics showed that the Asp179Asn variant of KPC-2 demonstrated enhanced kinetic properties against ceftazidime. The Ki app, k2/K and koff of the Arg164Ala and Asp179Asn variant KPC-2 β-lactamases indicated that avibactam effectively inhibited these enzymes. Conclusions Several KPC-2 variants demonstrating ceftazidime resistance as a result of single amino acid substitutions in the Ω-loop were not susceptible to ceftazidime/avibactam (MICs >8 mg/L). We hypothesize that this observation is due to the stabilizing interactions (e.g. hydrogen bonds) of ceftazidime within the active site of variant β-lactamases that prevent avibactam from binding to and inhibiting the β-lactamase. As ceftazidime/avibactam is introduced into the clinic, monitoring for new KPC-2 variants that may exhibit increased ceftazidime kinetics as well as resistance to this novel antibiotic combination will be important. PMID:25957381

  9. Solid state and sub-cooled liquid vapour pressures of substituted dicarboxylic acids using Knudsen Effusion Mass Spectrometry (KEMS and Differential Scanning Calorimetry

    A. M. Booth

    2010-02-01

    Full Text Available Solid state vapour pressures of a selection of substituted dicarboxylic acids have been measured using Knudsen Effusion Mass Spectrometry (KEMS. Enthalpies of fusion and melting points obtained using Differential Scanning Calorimetry (DSC were used to obtain sub-cooled liquid vapour pressures. They have been compared to estimation methods used on the E-AIM website. These methods are shown to poorly represent -OH groups in combination with COOH groups. Partitioning calculations have been performed to illustrate the impact of the different estimation methods on organic aerosol mass compared to the use of experimental data.

  10. Solid state and sub-cooled liquid vapour pressures of substituted dicarboxylic acids using Knudsen Effusion Mass Spectrometry (KEMS and Differential Scanning Calorimetry

    A. M. Booth

    2010-05-01

    Full Text Available Solid state vapour pressures of a selection of atmospherically important substituted dicarboxylic acids have been measured using Knudsen Effusion Mass Spectrometry (KEMS over a range of 20 K (298–318 K. Enthalpies of fusion and melting points obtained using Differential Scanning Calorimetry (DSC were used to obtain sub-cooled liquid vapour pressures. They have been compared to estimation methods used on the E-AIM website. These methods are shown to poorly represent – OH groups in combination with COOH groups. Partitioning calculations have been performed to illustrate the impact of the different estimation methods on organic aerosol mass compared to the use of experimental data.

  11. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

    Yang, Ziheng; Nielsen, Rasmus

    2008-01-01

    Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we...... to examine the null hypothesis that codon usage is due to mutation bias alone, not influenced by natural selection. Application of the test to the mammalian data led to rejection of the null hypothesis in most genes, suggesting that natural selection may be a driving force in the evolution of synonymous...... codon usage in mammals. Estimates of selection coefficients nevertheless suggest that selection on codon usage is weak and most mutations are nearly neutral. The sensitivity of the analysis on the assumed mutation model is discussed....

  12. Structure-Acidity-IR Spectra Correlations for p-Substituted N-Phenylsulfonylbenzamidesâ€

    Zora Sustekova

    2004-03-01

    Full Text Available The wavenumbers of the IR absorption bands of the C=O, S=O and N-H stretching vibrations for a series of p-substituted N-phenylsulfonylbenzamides were measured in trichloromethane. The bond orders, Mulliken charges, charge densities and heats of formation were calculated using the PM3 method. Fifty significant mutual mono parameter (MP and six dual parameter (DP correlations were found for the IR spectral, theoretical structural data, substituent constants and previously reported dissociation constants in five polar organic solvents. The transmission of the substituent effects has been discussed and the solvent effect on the slopes of some linear correlations was evaluated using different solvent parameters. The results showed that the factors describing the electronic structure and controlling the dissociation equilibrium and the IR spectra properties of p-substituted N-phenylsulfonylbenzamides must be the same

  13. Aqueous solubility study of salts of benzylamine derivatives and p-substituted benzoic acid derivatives using X-ray crystallographic analysis

    Parshad, Henrik; Frydenvang, Karla Andrea; Liljefors, Tommy;

    2004-01-01

    than those reported for the corresponding salts of benzylamine (I). Thermal analysis indicated that the increased solubility was caused by reduced crystal lattice energy, which was most likely due to the reduced number of strong hydrogen bonds of the salt of (II) and (III). X-ray crystallographic...... analysis of p-hydroxybenzoic acid salt of (I), (II) and (III) suggested that the reduced number of hydrogen bonds caused the apparent higher solubility. Further analyses of seven salts of (I) were performed. It was not possible to identify any relationship between the number of hydrogen bonds......Twenty two p-substituted benzoic acid derivates were used to prepare salts of N-methylbenzylamine (II) and N,N-dimethylbenzylamine (III), respectively. Only five salts of (II) and two salts of (III) were obtained in a crystalline state. The solubility of these salts was orders of magnitude higher...

  14. 取代苯氧乙酸的合成及生物活性研究%Synthesis and Biological Activities of Substituted Phenoxyacetic Acids

    许元明; 曾振芳

    2012-01-01

    Five substituted phenoxyacetic acids were prepared from corresponding phenols and chloroacetic acid catalyzed by PEG-800 in alkaline water. Their structures were confirmed by IR, 'H NMR and elemental analysis. The preliminary biological activities detection indicated that the compounds showed fungicidal activities to four vegetable pathogens at different extent.%以碱性水溶液为溶剂,以聚乙二醇-800为催化剂,一氯乙酸与5种取代苯酚合成了5种取代苯氧乙酸.各化合物结构经IR、1H NMR、元素分析进行表征,并对5种化合物进行了初步的室内生物活性测定,结果表明所合成的大部分化合物对所测菌种都有抑制作用.

  15. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

    Li Karen

    2008-12-01

    Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

  16. The efficacy of poly-d,l-lactic acid- and hyaluronic acid-coated bone substitutes on implant fixation in sheep

    Christina M. Andreasen

    2017-01-01

    Conclusion: This study demonstrates that HA/βTCP granules coated with PDLLA and HyA have similar bone ingrowth and implant fixation as those with allograft, and with mechanical properties resembling those of allograft in advance, they may be considered as alternative substitute materials for bone formation in sheep.

  17. Biological activity of novel N-substituted amides of endo-3-(3-methylthio-1,2,4-triazol-5-yl)bicyclo[2.2.1]hept-5-ene-2-carboxylic acid and N-substituted amides of 1-(5-methylthio-1,2,4-triazol-3-yl)cyclohexane-2-carboxylic acids.

    Pachuta-Stec, Anna; Kosikowska, Urszula; Chodkowska, Anna; Pitucha, Monika; Malm, Anna; Jagiełło-Wójtowicz, Ewa

    2012-01-01

    N-Substituted amides of endo-3-(3-methylthio-1,2,4-triazol-5-yl)bicyclo[2.2.1]hept-5-ene-2-carboxylic acid and 1-(5-methylthio-1,2,4-triazol-3-yl)cyclohexane-2-carboxylic acid were prepared by the condensation reaction of endo-S-methyl-N1-(bicyclo[2.2.1]hept-5-ene-2,3-dicarbonyl)isothiosemicarbazide and S-methyl-N1-(cyclohexane-2,3-dicarbonyl)isothiosemicarbazide with primary amines. The synthesized compounds were screened for their microbiological and pharmacological activities.

  18. Competitive Fitness of Influenza B Viruses with Neuraminidase Inhibitor-Resistant Substitutions in a Coinfection Model of the Human Airway Epithelium

    Burnham, Andrew J.; Armstrong, Jianling; Lowen, Anice C.; Webster, Robert G.

    2015-01-01

    significant portion of seasonal influenza virus infections worldwide. The development of resistance to a single class of available antivirals, the neuraminidase (NA) inhibitors (NAIs), is a public health concern. Amino acid substitutions in the NA glycoprotein of influenza B virus not only can confer antiviral resistance but also can alter viral fitness. Here we used normal human bronchial epithelial (NHBE) cells, a model of the human upper respiratory tract, to examine the replicative capacities and fitness of NAI-resistant influenza B viruses. We show that virus with an E119A NA substitution can replicate efficiently in NHBE cells in the presence of oseltamivir or zanamivir and that virus with the H274Y NA substitution has a relative fitness greater than that of the wild-type NAI-susceptible virus. This study is the first to use NHBE cells to determine the fitness of NAI-resistant influenza B viruses. PMID:25673705

  19. Financial mechanisms and social safety-oriented model of development of the Russian economy (based on import substitution and innovation

    T. I. Ovchinnikova

    2016-01-01

    Full Text Available In article features of import substitution in the socially oriented model determined as economy with the high level of the state income redistribution of subjects of managing and developed on this basis of system of social protection are considered. Import substitution is considered from the traditional point of view – creation of new productions and technologies which are implemented at the expense of own and borrowed funds of investors. The financial mechanisms for implementation of innovations promoting import substitution are offered: industry plans and road maps as availability of reference points for creation of rational amounts of the budget payments and financial resources of the entities necessary for upgrade of productions, and also the directions of financial resources for implementation of specific most important national priorities and innovative investment projects. The volume of investment into the fixed capital correlated to its cost considerably grew from 3.5% in 2003 to 11.6% in 2009, but value of this indicator isn't enough as degree of depreciation of fixed assets in economy of the region constituted 44.9% in 2009. Direct foreign investments prevail: in Krasnoyarsk Krai their share constituted in 2009 – 45.4%, Krasnodar Region – 40.5%, the Nizhny Novgorod Region – 84.5%. In the Voronezh region such entities as KBHA, Federal State Unitary Enterprise State Research and Production Space Center branch of M. V. Khrunichev the Voronezh Mechanical Plant, JSC Sozvezdiye Concern having the high technologies making safety of the country and especially needing investments function. In plans of urgent strategy of social and economic development of the Voronezh region it is supposed to increase specific weight of innovative products of such entities and to increase the level of innovative activity till 2020. The socially oriented model considering import substitution domestic technologies and products needs strengthening of the

  20. Organic acid modeling and model validation: Workshop summary. Final report

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E&S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled ``Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.`` The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  1. Organic acid modeling and model validation: Workshop summary

    Sullivan, T.J.; Eilers, J.M.

    1992-08-14

    A workshop was held in Corvallis, Oregon on April 9--10, 1992 at the offices of E S Environmental Chemistry, Inc. The purpose of this workshop was to initiate research efforts on the entitled Incorporation of an organic acid representation into MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using Independent data sources.'' The workshop was attended by a team of internationally-recognized experts in the fields of surface water acid-bass chemistry, organic acids, and watershed modeling. The rationale for the proposed research is based on the recent comparison between MAGIC model hindcasts and paleolimnological inferences of historical acidification for a set of 33 statistically-selected Adirondack lakes. Agreement between diatom-inferred and MAGIC-hindcast lakewater chemistry in the earlier research had been less than satisfactory. Based on preliminary analyses, it was concluded that incorporation of a reasonable organic acid representation into the version of MAGIC used for hindcasting was the logical next step toward improving model agreement.

  2. Precise investigation of the axial ligand substitution mechanism on a hydrogenphosphato-bridged lantern-type platinum(III) binuclear complex in acidic aqueous solution.

    Iwatsuki, Satoshi; Mizushima, Chiho; Morimoto, Naoyuki; Muranaka, Shinji; Ishihara, Koji; Matsumoto, Kazuko

    2005-10-31

    Detailed equilibrium and kinetic studies on axial water ligand substitution reactions of the "lantern-type" platinum(III) binuclear complex, [Pt(2)(mu-HPO(4))(4)(H(2)O)(2)](2)(-), with halide and pseudo-halide ions (X(-) = Cl(-), Br(-), and SCN(-)) were carried out in acidic aqueous solution at 25 degrees C with I = 1.0 M. The diaqua Pt(III) dimer complex is in acid dissociation equilibrium in aqueous solution with -log K(h1) = 2.69 +/- 0.04. The consecutive formation constants of the aquahalo complex () and the dihalo complex () were determined spectrophotometrically to be log = 2.36 +/- 0.01 and log = 1.47 +/- 0.01 for the reaction with Cl(-) and log = 2.90 +/- 0.04 and log = 2.28 +/- 0.01 for the reaction with Br(-), respectively. In the kinetic measurements carried out under the pseudo-first-order conditions with a large excess concentration of halide ion compared to that of Pt(III) dimer (C(X)()- > C(Pt)), all of the reactions proceeded via a one-step first-order reaction, which is a contrast to the consecutive two-step reaction for the amidato-bridged platinum(III) binuclear complexes. The conditional first-order rate constant (k(obs)) depended on C(X)()- as well as the acidity of the solution. From kinetic analyses, the rate-limiting step was determined to be the first substitution process that forms the monohalo species, which is in rapid equilibrium with the dihalo complex. The reaction with 4-penten-1-ol was also kinetically investigated to examine the reactivity of the lantern complex with olefin compounds.

  3. Substitutional analysis

    Rutherford, Daniel Edwin

    2013-01-01

    Classic monograph, suitable for advanced undergraduates and graduate students. Topics include calculus of permutations and tableaux, semi-normal representation, orthogonal and natural representations, group characters, and substitutional equations. 1968 edition.

  4. Binary Mixtures of Nonyl Phenol with Alkyl Substituted Anilines as Corrosion Inhibitors for Mild Steel in Acidic Medium

    H. S. Shukla

    2012-01-01

    Full Text Available The present study deals with the evaluation of the corrosion inhibition effectiveness of the two binary mixtures of nonyl phenol (NPH with 2, 4 dimethyl aniline (DMA and 2 ethyl aniline (EA at different concentration ratios (from 1:7 to 7:1 for mild steel in H2SO4 (pH=1 solution by weight loss and potentiodynamic polarization method. Corrosion inhibition ability of the compounds has been tested at different exposure periods (6 h to 24 h and at different temperatures (303 K to 333 K. The binary mixture of NPH and EA (at 7:1 concentration ratio has afforded maximum inhibition (IE% 93.5% at 6 h exposure period and at room temperature. The adsorption of both the inhibitors is found to accord with Temkin adsorption isotherm. Potentiodynamic polarization study reveals that the tested inhibitors are mixed type inhibitor and preferentially act on cathodic areas. Electrochemical impedance study suggests formation of an inhibition layer by the adsorption of the inhibitors on the metal surface. An adsorption model of the inhibitor molecules on the metal surface has been proposed after immersion test in the inhibited acid showed characteristic shift of N-H and O-H bond frequencies towards lower side compared to that of the respective pure samples which indicated the donation of electron pair through N and O atom of the inhibitor molecule in the surface adsorption phenomena. SEM study has revealed formation of semi globular inhibitor products on the metal surface. The comparisons of the protection efficiencies of these compounds according to their relative electron density on the adsorption centre and projected molecular area of the inhibitor molecules have been made.

  5. Substitution in Amino Acid 70 of Hepatitis C Virus Core Protein Changes the Adipokine Profile via Toll-Like Receptor 2/4 Signaling.

    Satoko Uraki

    Full Text Available It has been suggested that amino acid (aa substitution at position 70 from arginine (70R to glutamine (70Q in the genotype 1b hepatitis C virus (HCV core protein is associated with insulin resistance and worse prognosis. However, the precise mechanism is still unclear. The aim of this study was to investigate the impact of the substitution at position 70 in HCV core protein on adipokine production by murine and human adipocytes.The influence of treatment with HCV core protein (70R or 70Q on adipokine production by both 3T3-L1 and human adipocytes were examined with real-time PCR and enzyme-linked immunosorbent assay (ELISA, and triglyceride content was also analyzed. The effects of toll-like receptor (TLR2/4 inhibition on IL-6 production by 3T3-L1 induced by HCV core protein were examined.IL-6 production was significantly increased and adiponectin production was reduced without a change in triglyceride content by treatment with 70Q compared to 70R core protein in both murine and human adipocytes. IL-6 induction of 3T3-L1 cells treated by 70Q HCV core protein was significantly inhibited with anti-TLR2 antibody by 42%, and by TLR4 inhibitor by 40%.Our study suggests that extracellular HCV core protein with substitution at position 70 enhanced IL-6 production and reduced adiponectin production from visceral adipose tissue, which can cause insulin resistance, hepatic steatosis, and ultimately development of HCC.

  6. Identification of robust synthon in the molecular salts of 2-aminothiazole with substituted benzoic acids: A case stu

    Madhavi Oruganti; Raghavaiah Pallepogu; Darshak R Trivedi

    2014-09-01

    Six new salts of an API intermediate 2-aminothiazole with different carboxylic acid coformers were synthesized and characterized by IR (Infrared spectroscopy), 1H-NMR, DSC (Differential scanning calorimetry), XRPD (X-ray powder diffraction) and single crystal XRD. The crystal structure of the salts with benzoic acid, 2,3-, 2,4-, 2,5-, 2,6- dihydroxybenzoic acids and 2,4-dinitrobenzoic acid were determined. The thiazole moiety exhibited solvent (polarity) assisted tautomerism in all reported salts and proton transfer was noticed to the ring N of thiazole due to which two point supramolecular synthon N+−H(thiazole)…O−(acid), N−H(amine)…O−(acid) was observed. The crystal structures were studied with respect to the positional effect of the competing functional groups like hydroxyl (−OH) and nitro (−NO2) as well as their donor and acceptor abilities for hydrogen bonding. The presence of the non-conventional hydrogen bond (C−H…O) has been found to play a critical role in the formation of secondary supramolecular architectures.

  7. Modulating the electronic structure of amino acids: interaction of model lewis acids with anthranilic acid

    Tareq Irshaidat

    2014-01-01

    Full Text Available On the basis of theoretical B3LYP calculations, Yáñez and co-workers (J. Chem. Theory Comput. 2012, 8, 2293 illustrated that beryllium ions are capable of significantly modulating (changing the electronic structures of imidazole. In this computational organic chemistry study, the interaction of this β-amino acid and five model Lewis acids (BeF1+, Be2+, AlF2(1+, AlF2+, and Al3+ were investigated. Several aspects were addressed: natural bond orbitals, including second order perturbation analysis of intra-molecular charge delocalization and the natural population analysis atomic charges; molecular geometries; selected infrared stretching frequencies (C-N, C-O, and N-H, and selected ¹H-NMR chemical shifts. The data illustrate that this interaction can weaken the H-O bond and goes beyond strengthening the intra-molecular hydrogen bond (N...H-O to cause a spontaneous transfer of the proton to the nitrogen atom in five cases generating zwitterion structures. Many new features are observed. Most importantly, the zwitterion structures include a stabilizing hydrogen bond (N-H...O that varies in relative strength according to the Lewis acid. These findings explain the experimental observations of α-amino acids (for example: J. Am. Chem. Soc. 2001, 123, 3577 and are the first reported fundamental electronic structure characterization of β-amino acids in zwitterion form.

  8. Ultra-superovulation for the CRISPR-Cas9-mediated production of gene-knockout, single-amino-acid-substituted, and floxed mice.

    Nakagawa, Yoshiko; Sakuma, Tetsushi; Nishimichi, Norihisa; Yokosaki, Yasuyuki; Yanaka, Noriyuki; Takeo, Toru; Nakagata, Naomi; Yamamoto, Takashi

    2016-08-15

    Current advances in producing genetically modified mice using genome-editing technologies have indicated the need for improvement of limiting factors including zygote collection for microinjection and their cryopreservation. Recently, we developed a novel superovulation technique using inhibin antiserum and equine chorionic gonadotropin to promote follicle growth. This method enabled the increased production of fertilized oocytes via in vitro fertilization compared with the conventional superovulation method. Here, we verify that the ultra-superovulation technique can be used for the efficient generation of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated knockout mice by microinjection of plasmid vector or ribonucleoprotein into zygotes. We also investigated whether single-amino-acid-substituted mice and conditional knockout mice could be generated. Founder mice bearing base substitutions were generated more efficiently by co-microinjection of Cas9 protein, a guide RNA and single-stranded oligodeoxynucleotide (ssODN) than by plasmid microinjection with ssODN. The conditional allele was successfully introduced by the one-step insertion of an ssODN designed to carry an exon flanked by two loxP sequences and homology arms using a double-cut CRISPR-Cas9 strategy. Our study presents a useful method for the CRISPR-Cas9-based generation of genetically modified mice from the viewpoints of animal welfare and work efficiency.

  9. Substitution Models of Water for Other Beverages, and the Incidence of Obesity and Weight Gain in the SUN Cohort

    Ujué Fresán

    2016-10-01

    Full Text Available Obesity is a major epidemic for developed countries in the 21st century. The main cause of obesity is energy imbalance, of which contributing factors include a sedentary lifestyle, epigenetic factors and excessive caloric intake through food and beverages. A high consumption of caloric beverages, such as alcoholic or sweetened drinks, may particularly contribute to weight gain, and lower satiety has been associated with the intake of liquid instead of solid calories. Our objective was to evaluate the association between the substitution of a serving per day of water for another beverage (or group of them and the incidence of obesity and weight change in a Mediterranean cohort, using mathematical models. We followed 15,765 adults without obesity at baseline. The intake of 17 beverage items was assessed at baseline through a validated food-frequency questionnaire. The outcomes were average change in body weight in a four-year period and new-onset obesity and their association with the substitution of one serving per day of water for one of the other beverages. During the follow-up, 873 incident cases of obesity were identified. In substitution models, the consumption of water instead of beer or sugar-sweetened soda beverages was associated with a lower obesity incidence (the Odds Ratio (OR 0.80 (95% confidence interval (CI 0.68 to 0.94 and OR 0.85 (95% CI 0.75 to 0.97; respectively and, in the case of beer, it was also associated with a higher average weight loss (weight change difference = −328 g; (95% CI −566 to −89. Thus, this study found that replacing one sugar-sweetened soda beverage or beer with one serving of water per day at baseline was related to a lower incidence of obesity and to a higher weight loss over a four-year period time in the case of beer, based on mathematical models.

  10. Substitution Models of Water for Other Beverages, and the Incidence of Obesity and Weight Gain in the SUN Cohort

    Fresán, Ujué; Gea, Alfredo; Bes-Rastrollo, Maira; Ruiz-Canela, Miguel; Martínez-Gonzalez, Miguel A.

    2016-01-01

    Obesity is a major epidemic for developed countries in the 21st century. The main cause of obesity is energy imbalance, of which contributing factors include a sedentary lifestyle, epigenetic factors and excessive caloric intake through food and beverages. A high consumption of caloric beverages, such as alcoholic or sweetened drinks, may particularly contribute to weight gain, and lower satiety has been associated with the intake of liquid instead of solid calories. Our objective was to evaluate the association between the substitution of a serving per day of water for another beverage (or group of them) and the incidence of obesity and weight change in a Mediterranean cohort, using mathematical models. We followed 15,765 adults without obesity at baseline. The intake of 17 beverage items was assessed at baseline through a validated food-frequency questionnaire. The outcomes were average change in body weight in a four-year period and new-onset obesity and their association with the substitution of one serving per day of water for one of the other beverages. During the follow-up, 873 incident cases of obesity were identified. In substitution models, the consumption of water instead of beer or sugar-sweetened soda beverages was associated with a lower obesity incidence (the Odds Ratio (OR) 0.80 (95% confidence interval (CI) 0.68 to 0.94) and OR 0.85 (95% CI 0.75 to 0.97); respectively) and, in the case of beer, it was also associated with a higher average weight loss (weight change difference = −328 g; (95% CI −566 to −89)). Thus, this study found that replacing one sugar-sweetened soda beverage or beer with one serving of water per day at baseline was related to a lower incidence of obesity and to a higher weight loss over a four-year period time in the case of beer, based on mathematical models. PMID:27809239

  11. Substitution Models of Water for Other Beverages, and the Incidence of Obesity and Weight Gain in the SUN Cohort.

    Fresán, Ujué; Gea, Alfredo; Bes-Rastrollo, Maira; Ruiz-Canela, Miguel; Martínez-Gonzalez, Miguel A

    2016-10-31

    Obesity is a major epidemic for developed countries in the 21st century. The main cause of obesity is energy imbalance, of which contributing factors include a sedentary lifestyle, epigenetic factors and excessive caloric intake through food and beverages. A high consumption of caloric beverages, such as alcoholic or sweetened drinks, may particularly contribute to weight gain, and lower satiety has been associated with the intake of liquid instead of solid calories. Our objective was to evaluate the association between the substitution of a serving per day of water for another beverage (or group of them) and the incidence of obesity and weight change in a Mediterranean cohort, using mathematical models. We followed 15,765 adults without obesity at baseline. The intake of 17 beverage items was assessed at baseline through a validated food-frequency questionnaire. The outcomes were average change in body weight in a four-year period and new-onset obesity and their association with the substitution of one serving per day of water for one of the other beverages. During the follow-up, 873 incident cases of obesity were identified. In substitution models, the consumption of water instead of beer or sugar-sweetened soda beverages was associated with a lower obesity incidence (the Odds Ratio (OR) 0.80 (95% confidence interval (CI) 0.68 to 0.94) and OR 0.85 (95% CI 0.75 to 0.97); respectively) and, in the case of beer, it was also associated with a higher average weight loss (weight change difference = -328 g; (95% CI -566 to -89)). Thus, this study found that replacing one sugar-sweetened soda beverage or beer with one serving of water per day at baseline was related to a lower incidence of obesity and to a higher weight loss over a four-year period time in the case of beer, based on mathematical models.

  12. 氮杂冠醚化双Schiff碱配合物催化羧酸酯水解的研究%Study on aza crown ether substituted bis-Schiff base complexes catalyze carboxylic acid esters hydrolysis

    程杰; 李建章; 何锡阳; 曾俊; 肖正华; 胡伟

    2012-01-01

    将4种氮杂冠醚取代的双Schiff碱钴(H)、锰(m)配合物作为仿水解酶模型催化羧酸酯(PNPP)水解.考察了Schiff碱配合物中氮杂冠醚取代的位置、氮杂冠醚的数目对其仿水解酶性能的影响;探讨了Schiff配合物催化PNPP水解的动力学和机理;提出了配合物催化PNPP水解的动力学模型.结果表明,在25℃条件下随着缓冲溶液pH值的增大,配合物催化PNPP水解速率提高;四种氮杂冠醚取代的双Schiff碱配合物在催化PNPP水解反应中表现出良好的催化活性;氮杂冠醚3-取代的Schiff碱配合物CoL2的催化活性高于5-取代的Schiff碱配合物CoL1,含有2个氮杂冠醚的配合物CoL3的催化活性高于含有1个氮杂冠醚的配合物CoL2.%Four aza crown ether substituted bis-Schiff base transition-mental complexes have been used as mimic hydrolytic enzyme model catalyzing carboxylic acid esters ( PNPP) hydrolysis. The effects of substituted position of aza-crown and amount of aza-crown of Schiff base complexes were studied. The kinetics on PNPP hydrolysis catalyzed by these complexes was investigated. The kinetic mathematical model of PNPP cleavage catalyzed by these complexes was proposed. The results showed that the rate for the catalytic PNPP hydrolysis was increased following the increase of pH of the buffer solution; four complexes exhibited high activity in the catalytic PNPP hydrolysis, The catalytic activity of unsymmetrical Schiff base complexes of 3-substitute benzo-10-aza-crown groups ( CoL2 ) is larger than that of 5 -substitute benzo-10-aza-crown groups ( CoL1) , and the catalytic activity of Schiff base complexes with two benzo-10-aza-crown ether pendants (CoL3) is larger than that of Schiff base complexes with one benzo-10-aza-crown ether pendants (CoL2).

  13. Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.

    Brandt, Gabriel S; Nemeria, Natalia; Chakraborty, Sumit; McLeish, Michael J; Yep, Alejandra; Kenyon, George L; Petsko, Gregory A; Jordan, Frank; Ringe, Dagmar

    2008-07-22

    Benzaldehyde lyase (BAL) catalyzes the reversible cleavage of ( R)-benzoin to benzaldehyde utilizing thiamin diphosphate and Mg (2+) as cofactors. The enzyme is important for the chemoenzymatic synthesis of a wide range of compounds via its carboligation reaction mechanism. In addition to its principal functions, BAL can slowly decarboxylate aromatic amino acids such as benzoylformic acid. It is also intriguing mechanistically due to the paucity of acid-base residues at the active center that can participate in proton transfer steps thought to be necessary for these types of reactions. Here methyl benzoylphosphonate, an excellent electrostatic analogue of benzoylformic acid, is used to probe the mechanism of benzaldehyde lyase. The structure of benzaldehyde lyase in its covalent complex with methyl benzoylphosphonate was determined to 2.49 A (Protein Data Bank entry 3D7K ) and represents the first structure of this enzyme with a compound bound in the active site. No large structural reorganization was detected compared to the complex of the enzyme with thiamin diphosphate. The configuration of the predecarboxylation thiamin-bound intermediate was clarified by the structure. Both spectroscopic and X-ray structural studies are consistent with inhibition resulting from the binding of MBP to the thiamin diphosphate in the active centers. We also delineated the role of His29 (the sole potential acid-base catalyst in the active site other than the highly conserved Glu50) and Trp163 in cofactor activation and catalysis by benzaldehyde lyase.

  14. Synthesis and antimicrobial evaluation of L-phenylalanine-derived C5-substituted rhodanine and chalcone derivatives containing thiobarbituric acid or 2-thioxo-4-thiazolidinone.

    Jin, Xin; Zheng, Chang-Ji; Song, Ming-Xia; Wu, Yan; Sun, Liang-Peng; Li, Yin-Jing; Yu, Li-Jun; Piao, Hu-Ri

    2012-10-01

    Four novel series of compounds, including the l-phenylalanine-derived C5-substituted rhodanine (6a-q, 7a-j) and chalcone derivatives containing thiobarbituric acid or 2-thioxo-4-thiazolidinone (9a-e, 11a-e) have been designed, synthesized, characterized, and evaluated for their antibacterial activity. Some of these compounds showed significant antibacterial activity against Gram-positive bacterias, especially against the strains of multidrug-resistant clinical isolates, among which compounds 6c-e, 6g, 6i, 6j and 6q exhibiting high levels of antimicrobial activity against Staphylococcus aureus RN4220 with minimum inhibitory concentration (MIC) values of 2 μg/mL. Compound 6q showed the most potent activity of all of the compounds against all of the test multidrug-resistant clinical isolates tested. Unfortunately, however, none of the compounds were active against Gram-negative bacteria at 64 μg/mL.

  15. Silica sulfuric acid: a reusable solid catalyst for one pot synthesis of densely substituted pyrrole-fused isocoumarins under solvent-free conditions

    Sudipta Pathak

    2013-11-01

    Full Text Available A convenient and efficient methodology for the synthesis of densely substituted pyrrole-fused isocoumarins, which employs solid-supported silica sulfuric acid (SSA as catalyst, has been developed. When the mixture of ninhydrin adducts of acetylacetone/ethyl acetoacetate and primary amines was heated on the solid surface of SSA under solvent-free conditions, the pyrrole-fused isocoumarins were formed in good yields. This synthetic method has several advantages such as the employment of solvent-free reaction conditions without the use of any toxic reagents and metal catalysts, the ease of product isolation, the use of a recyclable catalyst, the low cost, the easy availability of the starting materials, and the excellent yields of products.

  16. Long-chain ethers as solvents can amplify the enantioselectivity of the Carica papaya lipase-catalyzed transesterification of 2-(substituted phenoxy)propanoic acid esters.

    Miyazawa, Toshifumi; Iguchi, Wakana

    2013-10-01

    The enantioselectivity of the transesterification of the 2,2,2-trifluoroethyl esters of 2-(substituted phenoxy)propanoic acids, as catalyzed by the lipase from Carica papaya, was greatly improved by using long-chain ethers, such as di-n-hexyl ether, as solvents instead of the conventional diisopropyl ether. Thus, for example, the E value was enhanced from 21 [in diisopropyl ether (0.8 ml)] to 57 [in di-n-hexyl ether (0.8 ml)] in the reaction of 2,2,2-trifluoroethyl(RS)-2-phenoxypropanoate (0.1 mmol) with methanol (0.4 mmol) in the presence of the plant lipase preparation (10 mg); it was also improved from 13 (in diisopropyl ether) to 44 (in di-n-hexyl ether) in the reaction of 2,2,2-trifluoroethyl(RS)-2-(2-chlorophenoxy)propanoate with methanol under the same reaction conditions.

  17. The use of Liquid Smoke as A Substitute for Nitric Acid for Extraction of Amorphous silica from Rice husk through Sol-Gel Route

    Wasinton Simanjuntak

    2016-08-01

    Full Text Available This study assessed the potential of liquid smoke as substitute for nitric acid for production of rice husk silica using sol-gel method. The efficacy of liquid smoke was compared to that of 10% HNO3 solution in terms of the volume required and the mass of silica obtained. Further evaluation was made by comparing the characteristics of the silica as revealed by several characterization techniques include Fourier infrared spectroscopy, x-ray diffraction, scanning electron microscopy, and particle size analysis. No significant difference between the volume of the liquid smoke and the HNO3 solution required, as well as between the mass of silica obtained. Both samples display practically similar functionality and structure. The most interesting finding is that the silica obtained using liquid smoke exhibits more homogeneous surface morphology and narrower particle size distribution. Considering its environmentally friendly nature, it was concluded that liquid smoke is more advantageous than HNO3 solution.

  18. Effect of surface acidity and pore size of Al-substituted plugs-containing SBA-15 and MCM-41 silicas on the polymerization of THF

    Zhi Qi Jia; Ming Zhao; Chun Guang Gao; Yong Xiang Zhao

    2011-01-01

    We reported here the simultaneous influence of surface acidity and pore size of Al-substituted hexagonal mesoporous silicas (Aldoped plugs-containing SBA-15 and Al-doped MCM-41) on polymerization of THF.These materials were directly synthesized by introduced aluminum isopropoxide into reaction mixture including surfactant and siliceous precursor.Al-doped plugs-containing SBA-15 (denotes as PAS) samples not only possess typical two-step desorption isotherms,which implied PAS materials generated plugs in their mesochannel,but also exhibit larger pore size and thicker wall than that of Al-doped MCM-41 (denotes as ACM),which implied PAS would have a great advantage on catalytic reaction involving large molecular (e.g.polymer of TI-IF) in industrial point'of view.To investigate catalytic activity of PAS and ACM with moderate acidic sites the polymerization of THF in the presence of acetic anhydride was carded out.The results showed PAS exhibiting good performance on polymerization of THF.Such result could be related to the large pore size and moderate acidic sites.

  19. Proton conductivity and fuel cell property of composite electrolyte consisting of Cs-substituted heteropoly acids and sulfonated poly(ether-ether ketone)

    Oh, S.Y.; Yoshida, T.; Kawamura, G.; Sakai, M.; Matsuda, A. [Department of Materials Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580 (Japan); Muto, H. [Department of Materials Science and Engineering, Kurume National College of Technology, 1-1-1 Komorino, Kurume, Fukuoka 830-8555 (Japan)

    2010-09-15

    Inorganic-organic composite electrolytes were fabricated from partially Cs{sup +}-substituted heteropoly acids (Cs-HPAs) and sulfonated poly(ether-ether ketone) (SPEEK) for application in fuel cells. Heteropoly acids, such as phosphotungstic acid (H{sub 3}PW{sub 12}O{sub 40}:WPA), and silicotungstic acid (H{sub 4}SiW{sub 12}O{sub 40}:WSiA), were mechanochemically treated with cesium hydrogen sulfate (CsHSO{sub 4}) to obtain the form of Cs-HPAs. SPEEK was prepared from PEEK by sulfonation using concentrated sulfuric acid. Water durability and surface structure of HPAs were modified by introducing Cs{sup +} into HPAs. Flexible and hot water stable composite electrolytes were obtained, and their electrochemical properties were markedly improved with the addition of Cs-HPAs into the SPEEK matrix. Maximum power densities of 245 and 247 mW cm{sup -2} were obtained for 50WPA.50CsHSO{sub 4} and 50WSiA.50CsHSO{sub 4} in SPEEK (1/5 by weight) composite electrolytes, respectively, from single cell tests at 80 C and 80 RH%. These results suggest that a three-dimensional proton-conductive path was formed among homogeneously distributed Cs-HPAs particles in the SPEEK matrix. The Cs-HPAs incorporated into the SPEEK matrix increased the number of protonate sites in the electrolyte. These observations imply that the mechanochemically synthesized Cs-HPAs, which consist of hydrogen bondings between Cs-HPAs and -HSO{sub 4}{sup -}, dissociated from CsHSO{sub 4}, are promising materials as inorganic fillers in inorganic-organic composite. (author)

  20. Proton conductivity and fuel cell property of composite electrolyte consisting of Cs-substituted heteropoly acids and sulfonated poly(ether-ether ketone)

    Oh, S. Y.; Yoshida, T.; Kawamura, G.; Muto, H.; Sakai, M.; Matsuda, A.

    Inorganic-organic composite electrolytes were fabricated from partially Cs +-substituted heteropoly acids (Cs-HPAs) and sulfonated poly(ether-ether ketone) (SPEEK) for application in fuel cells. Heteropoly acids, such as phosphotungstic acid (H 3PW 12O 40:WPA), and silicotungstic acid (H 4SiW 12O 40:WSiA), were mechanochemically treated with cesium hydrogen sulfate (CsHSO 4) to obtain the form of Cs-HPAs. SPEEK was prepared from PEEK by sulfonation using concentrated sulfuric acid. Water durability and surface structure of HPAs were modified by introducing Cs + into HPAs. Flexible and hot water stable composite electrolytes were obtained, and their electrochemical properties were markedly improved with the addition of Cs-HPAs into the SPEEK matrix. Maximum power densities of 245 and 247 mW cm -2 were obtained for 50WPA·50CsHSO 4 and 50WSiA·50CsHSO 4 in SPEEK (1/5 by weight) composite electrolytes, respectively, from single cell tests at 80 °C and 80 RH%. These results suggest that a three-dimensional proton-conductive path was formed among homogeneously distributed Cs-HPAs particles in the SPEEK matrix. The Cs-HPAs incorporated into the SPEEK matrix increased the number of protonate sites in the electrolyte. These observations imply that the mechanochemically synthesized Cs-HPAs, which consist of hydrogen bondings between Cs-HPAs and -HSO 4 -, dissociated from CsHSO 4, are promising materials as inorganic fillers in inorganic-organic composite.

  1. Separation of Long and Short Chain Fatty Acids as Naphthacyl and Substituted Phenacyl Esters by High Performance Liquid Chromatography.

    High performance liquid chromatography of various C2 - C24 fatty acids was run on their p-bromophenacyl, p-nitrophenacyl, p-chlorophenacyl, and 2--naphthacyl esters. All the separations were accomplished using reversed phase columns with the eluent consisting of an acetonitrile:water gradient. For all derivatives tested the separations were well defined and analogous although certain esters eluted together as one peak. Quantitative results indicate that the limit of detection in the present study was two picograms of n-caproic acid and 10 picograms of

  2. Model development for naphthenic acids ozonation process.

    Al Jibouri, Ali Kamel H; Wu, Jiangning

    2015-02-01

    Naphthenic acids (NAs) are toxic constituents of oil sands process-affected water (OSPW) which is generated during the extraction of bitumen from oil sands. NAs consist mainly of carboxylic acids which are generally biorefractory. For the treatment of OSPW, ozonation is a very beneficial method. It can significantly reduce the concentration of NAs and it can also convert NAs from biorefractory to biodegradable. In this study, a factorial design (2(4)) was used for the ozonation of OSPW to study the influences of the operating parameters (ozone concentration, oxygen/ozone flow rate, pH, and mixing) on the removal of a model NAs in a semi-batch reactor. It was found that ozone concentration had the most significant effect on the NAs concentration compared to other parameters. An empirical model was developed to correlate the concentration of NAs with ozone concentration, oxygen/ozone flow rate, and pH. In addition, a theoretical analysis was conducted to gain the insight into the relationship between the removal of NAs and the operating parameters.

  3. Statistical thermodynamics of the collagen triple-helix/coil transition. Free energies for amino acid substitutions within the triple-helix.

    Doig, Andrew J

    2008-11-27

    Collagen sequences frequently deviate from the most thermally stable (Gly-Pro-Hyp)(n) pattern, with many mutations causing osteogenesis imperfecta (or "brittle bone disease"). The effects of collagen mutations have been studied in short peptides. The analysis of this work is problematic, however, as triple-helices fray from their ends, making the coil/triple-helix equilibrium non-two-state. Here, I develop a statistical thermodynamic model to handle this equilibrium that is applicable to peptides that follow the (G-X-Y)(n) pattern, where Gly is present at every third position and where all three chains are identical. Parameters for substitutions at each position are included, as well as a penalty for initiating triple-helix formation. The model is applied to equilibrium experimental data at 37 degrees C to show that the extension of a triple-helix by a three residue unit stabilizes the triple-helix by 0.76 kcal/mol for Gly-Pro-Hyp and 0.33 kcal/mol for Gly-Pro-Pro. The replacement of Hyp by Arg, Asp, or Trp destabilizes the triple-helix by 1.5, 2.4, and 2.9 kcal/mol, respectively, where the substitution is present once in each chain. The model can thus be used to quantitatively interpret data on collagen peptides, giving free energies that can help rationalize mutations that affect collagen stability, and to design new collagen sequences.

  4. Whole-body acid-base modeling revisited

    Ring, Troels; Nielsen, Søren

    2017-01-01

    The textbook account of whole-body acid-base balance in terms of endogenous acid production, renal net acid excretion and gastrointestinal alkali absorption which is the only comprehensive model around, has never been applied in clinical practice or been formally validated. In order to improve...... understanding of acid-base modeling, we managed to write up this conventional model as an expression solely on urine chemistry. Renal net acid excretion and endogenous acid production was already formulated in terms of urine chemistry, and we could from the literature also see gastrointestinal alkali absorption...

  5. Amino acid substitutions of Na,K-ATPase conferring decreased sensitivity to cardenolides in insects compared to mammals

    Dalla, S.; Swarts, H.G.P.; Koenderink, J.B.; Dobler, S.

    2013-01-01

    Mutagenesis analyses and a recent crystal structure of the mammalian Na,K-ATPase have identified amino acids which are responsible for high affinity binding of cardenolides (such as ouabain) which at higher doses block the enzyme in the phosphorylated state. Genetic analysis of the Na,K-ATPase of in

  6. Influence of amino acid substitutions in the leader peptide on maturation and secretion of mesentericin Y105 by Leuconostoc mesenteroides.

    Aucher, Willy; Lacombe, Christian; Héquet, Arnaud; Frère, Jacques; Berjeaud, Jean-Marc

    2005-03-01

    By site-specific mutagenesis, the hydrophobic conserved amino acids and the C-terminal GG doublet of the leader peptide of pre-mesentericin Y105 were demonstrated to be critical for optimal secretion of mesentericin Y105, as well as for the maturation of the pre-bacteriocin by the protease portion of the ABC transporter MesD.

  7. Novel high-affinity and selective biaromatic 4-substituted ¿-hydroxybutyric acid (GHB) analogues as GHB ligands

    Høg, Signe; Wellendorph, Petrine; Nielsen, Birgitte;

    2008-01-01

    Gamma-hydroxybutyrate (GHB) is a metabolite of gamma-aminobutyric acid (GABA) and has been proposed to function as a neurotransmitter or neuromodulator. GHB is used in the treatment of narcolepsy and is a drug of abuse. GHB binds to both GABA(B) receptors and specific high-affinity GHB sites...

  8. Identification and Structural Analysis of Amino Acid Substitutions that Increase the Stability and Activity of Aspergillus niger Glucose Oxidase.

    Julia Marín-Navarro

    Full Text Available Glucose oxidase is one of the most conspicuous commercial enzymes due to its many different applications in diverse industries such as food, chemical, energy and textile. Among these applications, the most remarkable is the manufacture of glucose biosensors and in particular sensor strips used to measure glucose levels in serum. The generation of ameliorated versions of glucose oxidase is therefore a significant biotechnological objective. We have used a strategy that combined random and rational approaches to isolate uncharacterized mutations of Aspergillus niger glucose oxidase with improved properties. As a result, we have identified two changes that increase significantly the enzyme's thermal stability. One (T554M generates a sulfur-pi interaction and the other (Q90R/Y509E introduces a new salt bridge near the interphase of the dimeric protein structure. An additional double substitution (Q124R/L569E has no significant effect on stability but causes a twofold increase of the enzyme's specific activity. Our results disclose structural motifs of the protein which are critical for its stability. The combination of mutations in the Q90R/Y509E/T554M triple mutant yielded a version of A. niger glucose oxidase with higher stability than those previously described.

  9. Venezuelan equine encephalitis emergence: Enhanced vector infection from a single amino acid substitution in the envelope glycoprotein

    Brault, Aaron C.; Powers, Ann M.; Ortiz, Diana; Estrada-Franco, Jose G.; Navarro-Lopez, Roberto; Weaver, Scott C.

    2004-01-01

    In 1993 and 1996, subtype IE Venezuelan equine encephalitis (VEE) virus caused epizootics in the Mexican states of Chiapas and Oaxaca. Previously, only subtype IAB and IC VEE virus strains had been associated with major outbreaks of equine and human disease. The IAB and IC epizootics are believed to emerge via adaptation of enzootic (sylvatic, equine-avirulent) strains for high titer equine viremia that results in efficient infection of mosquito vectors. However, experimental equine infections with subtype IE equine isolates from the Mexican outbreaks demonstrated neuro-virulence but little viremia, inconsistent with typical VEE emergence mechanisms. Therefore, we hypothesized that changes in the mosquito vector host range might have contributed to the Mexican emergence. To test this hypothesis, we evaluated the susceptibility of the most abundant mosquito in the deforested Pacific coastal locations of the VEE outbreaks and a proven epizootic vector, Ochlerotatus taeniorhynchus. The Mexican epizootic equine isolates exhibited significantly greater infectivity compared with closely related enzootic strains, supporting the hypothesis that adaptation to an efficient epizootic vector contributed to disease emergence. Reverse genetic studies implicated a Ser → Asn substitution in the E2 envelope glycoprotein as the major determinant of the increased vector infectivity phenotype. Our findings underscore the capacity of RNA viruses to alter their vector host range through minor genetic changes, resulting in the potential for disease emergence. PMID:15277679

  10. Molecular evolution of B6 enzymes: Binding of pyridoxal-5'-phosphate and Lys41Arg substitution turn ribonuclease A into a model B6 protoenzyme

    Marra Ersilia

    2008-06-01

    Full Text Available Abstract Background The pyridoxal-5'-phosphate (PLP-dependent or vitamin B6-dependent enzymes that catalyze manifold reactions in the metabolism of amino acids belong to no fewer than four evolutionarily independent protein families. The multiple evolutionary origin and the essential mechanistic role of PLP in these enzymes argue for the cofactor having arrived on the evolutionary scene before the emergence of the respective apoenzymes and having played a dominant role in the molecular evolution of the B6 enzyme families. Here we report on an attempt to re-enact the emergence of a PLP-dependent protoenzyme. The starting protein was pancreatic ribonuclease A (RNase, in which active-site Lys41 or Lys7 readily form a covalent adduct with PLP. Results We screened the PLP adduct of wild-type RNase and two variant RNases (K7R and K41R for catalytic effects toward L- and D-amino acids. RNase(K41R-PLP, in which the cofactor is bound through an imine linkage to Lys7, qualifies for a model proto-B6 enzyme by the following criteria: (1 covalent linkage of PLP (internal aldimine; (2 catalytic activity toward amino acids that depends on formation of an imine linkage with the substrate (external aldimine; (3 adjoining binding sites for the cofactor and amino acid moiety that facilitate the transimination reaction of the internal to the external aldimine and stabilize the resulting noncovalent complex of the coenzyme-substrate adduct with the protein; (4 reaction specificity, the only detectable reactions being racemization of diverse amino acids and β-decarboxylation of L-aspartate; (5 acceleration factors for racemization and β-decarboxylation of >103 over and above that of PLP alone; (6 ribonuclease activity that is 103-fold lower than that of wild-type RNase, attenuation of a pre-existing biological activity being indispensable for the further evolution as a PLP-dependent protoenzyme. Conclusion A single amino acid substitution (Lys41Arg and covalent

  11. Empirical codon substitution matrix

    Gonnet Gaston H

    2005-06-01

    Full Text Available Abstract Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.

  12. Molecular modelling of some para-substituted aryl methyl telluride and diaryl telluride antioxidants

    Frisell, H.; Engman, L.

    2000-08-01

    Quantum mechanical calculations using the 3-21G(d) basis-set were performed on some p-substituted diaryl tellurides and aryl methyl tellurides, and the corresponding cationic radicals of these compounds. Calculated relative radical stabilization energies (RSE:s) were shown to correlate with experimentally determined peak oxidation potentials ( R=0.93) and 125Te-NMR chemical shifts ( R=0.91). A good correlation was also observed between the RSE:s and the Mulliken charge at the tellurium atoms ( R=0.97). The results showed that Hartree-Fock calculations using the 3-21G(d) basis set was sufficiently accurate for estimating the impact of p-substituents in aryl tellurides on experimentally determined properties such as peak oxidation potentials and 125Te-NMR chemical shifts.

  13. Design, synthesis and biological evaluation of α-substituted isonipecotic acid benzothiazole analogues as potent bacterial type II topoisomerase inhibitors.

    Axford, Lorraine C; Agarwal, Piyush K; Anderson, Kelly H; Andrau, Laura N; Atherall, John; Barker, Stephanie; Bennett, James M; Blair, Michael; Collins, Ian; Czaplewski, Lloyd G; Davies, David T; Gannon, Carlie T; Kumar, Dushyant; Lancett, Paul; Logan, Alastair; Lunniss, Christopher J; Mitchell, Dale R; Offermann, Daniel A; Palmer, James T; Palmer, Nicholas; Pitt, Gary R W; Pommier, Stéphanie; Price, Daniel; Narasinga Rao, B; Saxena, Rashmi; Shukla, Tarun; Singh, Amit K; Singh, Mahipal; Srivastava, Anil; Steele, Christopher; Stokes, Neil R; Thomaides-Brears, Helena B; Tyndall, Edward M; Watson, David; Haydon, David J

    2013-12-15

    The discovery and optimisation of a new class of benzothiazole small molecules that inhibit bacterial DNA gyrase and topoisomerase IV are described. Antibacterial properties have been demonstrated by activity against DNA gyrase ATPase and potent activity against Staphylococcus aureus, Enterococcus faecalis, Streptococcus pyogenes and Haemophilus influenzae. Further refinements to the scaffold designed to enhance drug-likeness included analogues bearing an α-substituent to the carboxylic acid group, resulting in excellent solubility and favourable pharmacokinetic properties.

  14. Substituted ethan phosphonic acid esters as reagents for the separation of molybdenum from rhenium by solvent extraction.

    Jordanov, N; Mareva, S; Borisov, G; Jordanov, B

    1968-02-01

    New esters of the ethan phosphonic acids have been synthesized and their extraction properties studied with respect to Mo(VI), Re(VII), Fe(III),Au(III),Tl(III) and Sb(V). A possibility is shown for the analytical separation of molybdenum from rhenium (beta = 700). The state of these new extraction agents in carbon tetrachloride solution, and the mechanism of the extraction processes, have been investigated by means of infrared spectra.

  15. A novel {sup 99m}Tc-labeled dimethyl-substituted zoledronic acid (DMIDP) with improved bone imaging efficiency

    Qiu, L.; Lin, J.; Luo, S.; Wang, Y.; Cheng, W.; Zhang, S. [Jiangsu Institute of Nuclear Medicine, Wuxi (China). Key Laboratory of Nuclear Medicine

    2012-07-01

    A novel zoledronic acid (ZL) derivative, 1-hydroxy-2-(2,4-dimethyl-1H-imidazol-1-yl)-ethane-1,1-diyldiphosphonic acid (DMIDP, dimezoledronate), was successfully prepared and labeled with {sup 99m}Tc in a high labeling yield. The biodistribution in mice shows that {sup 99m}Tc-DMIDP has significant advantage regarding bone resorption and clearance from soft tissues compared with {sup 99m}Tc-ZL and the clinically widely-used bone-imaging agent {sup 99m}Tc-MDP (methylenediphosphonic acid). Kinetics of blood clearance displayed that distribution half-life (T{sub 1/2{alpha}}) and elimination half-life (T{sub 1/2{beta}}) of {sup 99m}Tc-DMIDP were 2.53 min and 23.53 min, while those of {sup 99m}Tc-ZL were 2.28 and 52.63 min, respectively. Excellent images of the rabbit skeleton can be quickly obtained from {sup 99m}Tc-DMIDP, which was faster than {sup 99m}Tc-ZL and {sup 99m}Tc-MDP. The present findings indicate that {sup 99m}Tc-DMIDP possesses excellent potential for application as a novel bone scanning agent. (orig.)

  16. Solvent substitution

    1990-01-01

    The DOE Environmental Restoration and Waste Management Office of Technology Development and the Air Force Engineering and Services Center convened the First Annual International Workshop on Solvent Substitution on December 4--7, 1990. The primary objectives of this joint effort were to share information and ideas among attendees in order to enhance the development and implementation of required new technologies for the elimination of pollutants associated with industrial use of hazardous and toxic solvents; and to aid in accelerating collaborative efforts and technology transfer between government and industry for solvent substitution. There were workshop sessions focusing on Alternative Technologies, Alternative Solvents, Recovery/Recycling, Low VOC Materials and Treatment for Environmentally Safe Disposal. The 35 invited papers presented covered a wide range of solvent substitution activities including: hardware and weapons production and maintenance, paint stripping, coating applications, printed circuit boards, metal cleaning, metal finishing, manufacturing, compliance monitoring and process control monitoring. This publication includes the majority of these presentations. In addition, in order to further facilitate information exchange and technology transfer, the US Air Force and DOE solicited additional papers under a general Call for Papers.'' These papers, which underwent review and final selection by a peer review committee, are also included in this combined Proceedings/Compendium. For those involved in handling, using or managing hazardous and toxic solvents, this document should prove to be a valuable resource, providing the most up-to-date information on current technologies and practices in solvent substitution. Individual papers are abstracted separated.

  17. Novel high-affinity and selective biaromatic 4-substituted gamma-hydroxybutyric acid (GHB) analogues as GHB ligands: design, synthesis, and binding studies.

    Høg, Signe; Wellendorph, Petrine; Nielsen, Birgitte; Frydenvang, Karla; Dahl, Ivar F; Bräuner-Osborne, Hans; Brehm, Lotte; Frølund, Bente; Clausen, Rasmus P

    2008-12-25

    Gamma-hydroxybutyrate (GHB) is a metabolite of gamma-aminobutyric acid (GABA) and has been proposed to function as a neurotransmitter or neuromodulator. GHB is used in the treatment of narcolepsy and is a drug of abuse. GHB binds to both GABA(B) receptors and specific high-affinity GHB sites in brain, of which the latter have not been linked unequivocally to function, but are speculated to be GHB receptors. In this study, a series of biaromatic 4-substituted GHB analogues, including 4'-phenethylphenyl, 4'-styrylphenyl, and 4'-benzyloxyphenyl GHB analogues, were synthesized and characterized pharmacologically in a [3H](E,RS)-(6,7,8,9-tetrahydro-5-hydroxy-5H-benzocyclohept-6-ylidene)acetic acid ([3H]NCS-382) binding assay and in GABA(A) and GABA(B) receptor binding assays. The compounds were selective for the high-affinity GHB binding sites and several displayed Ki values below 100 nM. The affinity of the 4-[4'-(2-iodobenzyloxy)phenyl] GHB analogue 17b was shown to reside predominantly with the R-enantiomer (Ki = 22 nM), which has higher affinity than previously reported GHB ligands.

  18. Impulsive mathematical modeling of ascorbic acid metabolism in healthy subjects.

    Bachar, Mostafa; Raimann, Jochen G; Kotanko, Peter

    2016-03-07

    In this work, we develop an impulsive mathematical model of Vitamin C (ascorbic acid) metabolism in healthy subjects for daily intake over a long period of time. The model includes the dynamics of ascorbic acid plasma concentration, the ascorbic acid absorption in the intestines and a novel approach to quantify the glomerular excretion of ascorbic acid. We investigate qualitative and quantitative dynamics. We show the existence and uniqueness of the global asymptotic stability of the periodic solution. We also perform a numerical simulation for the entire time period based on published data reporting parameters reflecting ascorbic acid metabolism at different oral doses of ascorbic acid.

  19. First principles calculations of hyperfine parameters on the Ca manganite with substitutional Cd-modeling of a PAC experiment

    Goncalves, JN; Lopes, A M L; Haas, H; Amaral, V S; Goncalves, J N

    2010-01-01

    The APW + lo (augmented plane waves + local orbitals) method of density functional theory, as implemented in the Wien2k code, is applied to calculate the electric field gradient of manganites. We report the first principles calculations on CaMnO3, and modeling of a perturbed angular correlation experiment with implanted Cd-111m isotope. To model the experiment we additionally calculate in Ca1-xCdxMnO3, where we substitute Cd at the Ca site. Increasing Cd dilution is done with the use of supercells. We find that the experimental CaMnO3 low-temperature value V-zz approximate to 6 x 10(-21) V/m(2) is reproduced, whenoptimizinginternalparameters. The analysis of the EFG tensor at the Ca atoms, with different electric field gradients at inequivalent positions, reveals that the convergence of the calculations is obtained. (C) 2009 Elsevier B.V. All rights reserved.

  20. The Effect of Ring Substitution Position on the Structural Conformation of Mercaptobenzoic Acid Self-Assembled Monolayers on Au(111)

    Lee, J; Willey, T; Nilsson, J; Terminello, L; De Yoreo, J; van Buuren, T

    2006-04-12

    Near edge X-ray absorption fine structure (NEX-AFS) spectroscopy, photoemission spectroscopy (PES) and contact angle measurements have been used to examine the structure and bonding of self-assembled monolayers (SAMs) prepared on Au(111) from the positional isomers of mercaptobenzoic acid (MBA). The isomer of MBA and solvent chosen in SAM preparation has considerable bearing upon film morphology. Carbon K-edge NEXAFS measurements indicate that the monomers of 2-, 3- and 4-MBA have well-defined orientations within their respective SAMs. Monomers of 3- and 4-MBA assume an upright orientation on the Au substrates in monolayers prepared using an acetic acid in ethanol solvent. The aryl ring and carboxyl group of these molecules are tilted from the surface normal by a colatitudal angle of {approx} 30{sup o}. Preparation of 4-MBA SAMs using pure ethanol solvent, a more traditional means of synthesis, had no appreciable effect upon the monomer orientation. Nonetheless, S(2p) PES measurements illustrate that it results in extensive bilayer formation via carboxyl group hydrogen-bonding between 4-MBA monomers. In 2-MBA monolayers prepared using acetic acid/ethanol solvent, the monomers adopt a more prostrate orientation on the Au substrates, in which the aryl ring and carboxyl group of the molecules are tilted {approx} 50{sup o} from the surface normal. This configuration is consistent with an interaction between both the mercaptan sulfur and carboxyl group of 2-MBA with the underlying substrate. S(2p) and C(1s) PES experiments provide supporting evidence for a bidentate interaction between 2-MBA and Au(111).

  1. Substitution of Ala564 in the first zinc cluster of the deoxyribonucleic acid (DNA)-binding domain of the androgen receptor by Asp, Asn, or Leu exerts differential effects on DNA binding

    H.T. Brüggenwirth (Hennie); A.L.M. Boehmer (Annemie); J.M. Lobaccaro; L. Chiche; C. Sultan; J. Trapman (Jan); A.O. Brinkmann (Albert)

    1998-01-01

    textabstractIn the androgen receptor of a patient with androgen insensitivity, the alanine residue at position 564 in the first zinc cluster of the DNA-binding domain was substituted by aspartic acid. In other members of the steroid receptor family, either valine or ala

  2. A codon substitution model that incorporates the effect of the GC contents, the gene density and the density of CpG islands of human chromosomes

    Misawa Kazuharu

    2011-08-01

    Full Text Available Abstract Background Developing a model for codon substitutions is essential for the analyses of protein sequences. Recent studies on the mutation rates in the non-coding regions have shown that CpG mutation rates in the human genome are negatively correlated to the local GC content and to the densities of functional elements. This study aimed at understanding the effect of genomic features, namely, GC content, gene density, and frequency of CpG islands, on the rates of codon substitution in human chromosomes. Results Codon substitution rates of CpG to TpG mutations, TpG to CpG mutations, and non-CpG transitions and transversions in humans were estimated by comparing the coding regions of thousands of human and chimpanzee genes and inferring their ancestral sequences by using macaque genes as the outgroup. Since the genomic features are depending on each other, partial regression coefficients of these features were obtained. Conclusion The substitution rates of codons depend on gene densities of the chromosomes. Transcription-associated mutation is one such pressure. On the basis of these results, a model of codon substitutions that incorporates the effect of genomic features on codon substitution in human chromosomes was developed.

  3. MCM-41-SO3H as a Highly Efficient Sulfonic Acid Nanoreactor for the Rapid and Green Synthesis of Some Novel Highly Substituted Imidazoles under Solvent-Free Condition

    Mahdavinia, Gholam Hossein; Amani, Ali Mohammad; Sepehrian, Hamid

    2012-01-01

    Nanosized MCM-41-SO3H based on ordered mesoporous silica material with a covalent sulfonic acid group was synthesized and used as acid catalyst for the new, simple, convenient and green synthesis of 2,4,5-trisubstituted and 1,2,4,5-tetra-substituted imidazoles. Also some of synthesis products are new. Echo-friendly protocol, short reaction times, easy and quick isolation of the products and excellent yields are the main advantages of this procedure.

  4. Design, Synthesis and Crystal Structures of 6-Alkylidene-2’-Substituted Penicillanic Acid Sulfones as Potent Inhibitors of Acinetobacter baumannii OXA-24 Carbapenemase

    Bou, German; Santillana, Elena; Sheri, Anjaneyulu; Beceiro, Alejandro; Sampson, Jared; Kalp, Matthew; Bethel, Christopher R.; Distler, Anne M.; Drawz, Sarah M.; Pagadala, Sundar Ram Reddy; van den Akker, Focco; Bonomo, Robert A.; Romero, Antonio; Buynak, John D.

    2010-01-01

    Class D β-lactamases represent a growing and diverse class of penicillin inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2’-substituted penicillanic acid sulfones (1, 2, 3, 4, and 5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC50 values, against OXA-24, and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs. WT) to 338 ± 20 nM (5 vs. Tyr112Ala, Met223Ala). Compound 4 possessed the lowest Ki (500 ± 80 nM vs. WT) and 1 possessed the highest inactivation efficiency (kinact/Ki = 0.21 ± 0.02 μM-1s-1). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal there is formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2’-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed. PMID:20822105

  5. Design, synthesis, and crystal structures of 6-alkylidene-2'-substituted penicillanic acid sulfones as potent inhibitors of Acinetobacter baumannii OXA-24 carbapenemase.

    Bou, German; Santillana, Elena; Sheri, Anjaneyulu; Beceiro, Alejandro; Sampson, Jared M; Kalp, Matthew; Bethel, Christopher R; Distler, Anne M; Drawz, Sarah M; Pagadala, Sundar Ram Reddy; van den Akker, Focco; Bonomo, Robert A; Romero, Antonio; Buynak, John D

    2010-09-29

    Class D β-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial β-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel β-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2'-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important β-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 β-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC(50) values against OXA-24 and two OXA-24 β-lactamase variants ranged from 10 ± 1 (4 vs WT) to 338 ± 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K(i) (500 ± 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k(inact)/K(i) = 0.21 ± 0.02 μM(-1)  s(-1)). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 Å) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2'-substituted penicillin sulfones are effective mechanism-based inactivators of class D β-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D β-lactamases is proposed.

  6. Synthesis, Antiproliferative and Antifungal Activities of 1,2,3-Triazole-Substituted Carnosic Acid and Carnosol Derivatives

    Mariano Walter Pertino

    2015-05-01

    Full Text Available Abietane diterpenes exhibit an array of interesting biological activities, which have generated significant interest among the pharmacological community. Starting from the abietane diterpenes carnosic acid and carnosol, twenty four new triazole derivatives were synthesized using click chemistry. The compounds differ in the length of the linker and the substituent on the triazole moiety. The compounds were assessed as antiproliferative and antifungal agents. The antiproliferative activity was determined on normal lung fibroblasts (MRC-5, gastric epithelial adenocarcinoma (AGS, lung cancer (SK-MES-1 and bladder carcinoma (J82 cells while the antifungal activity was assessed against Candida albicans ATCC 10231 and Cryptococcus neoformans ATCC 32264. The carnosic acid γ-lactone derivatives 1–3 were the most active antiproliferative compounds of the series, with IC50 values in the range of 43.4–46.9 μM and 39.2–48.9 μM for MRC-5 and AGS cells, respectively. Regarding antifungal activity, C. neoformans was the most sensitive fungus, with nine compounds inhibiting more than 50% of its fungal growth at concentrations ≤250 µg∙mL−1. Compound 22, possessing a p-Br-benzyl substituent on the triazole ring, showed the best activity (91% growth inhibition at 250 µg∙mL−1 In turn, six compounds inhibited 50% C. albicans growth at concentrations lower than 250 µg∙mL−1.

  7. Modeling the continuous lactic acid production process from wheat flour.

    Gonzalez, Karen; Tebbani, Sihem; Lopes, Filipa; Thorigné, Aurore; Givry, Sébastien; Dumur, Didier; Pareau, Dominique

    2016-01-01

    A kinetic model of the simultaneous saccharification, protein hydrolysis, and fermentation (SSPHF) process for lactic acid production from wheat flour has been developed. The model describes the bacterial growth, substrate consumption, lactic acid production, and maltose hydrolysis. The model was fitted and validated with data from SSPHF experiments obtained under different dilution rates. The results of the model are in good agreement with the experimental data. Steady state concentrations of biomass, lactic acid, glucose, and maltose as function of the dilution rate were predicted by the model. This steady state analysis is further useful to determine the operating conditions that maximize lactic acid productivity.

  8. Thermodynamic assessment of the Mg-Pb and Mg-Bi systems using substitutional solution and associate models for the liquid phase

    Zhang F.

    2014-01-01

    Full Text Available By means of CALPHAD approach, thermodynamic assessments of the Mg-Pb and Mg-Bi systems were carried out based on the available experimental data including thermodynamic properties and phase equilibrium data. The liquid phase was described with both the substitutional solution model and the associate model, and two sets of self-consistent thermodynamic parameters for the Mg-Pb and Mg-Bi systems were obtained, respectively. It was found that the associate model can account for the experimental data more satisfactorily than the substitutional solution one, especially for the liquid phase with the short-range order behavior.

  9. Substituting complements

    Dari-Mattiacci, G.; Parisi, F.; Heller, M.

    2009-01-01

    The presence of multiple sellers in the provision of (nonsubstitutable) complementary goods leads to outcomes that are worse than those generated by a monopoly (with a vertically integrated production of complements), a problem known in the economic literature as complementary oligopoly and recently popularized in the legal literature as the tragedy of the anticommons. We ask the following question: how many substitutes for each complement are necessary to render the presence of multiple sell...

  10. Diastereo- and enantioselective three-component coupling approach to highly substituted pyrrolidines.

    Chaulagain, Mani Raj; Felten, Albert E; Gilbert, Kevin; Aron, Zachary D

    2013-09-20

    The enantioselective synthesis of substituted pyrrolidines through a mild Lewis-acid catalyzed three-component coupling reaction between picolinaldehyde, amino acids, and activated olefins is reported. The reaction uses low catalyst loadings of commercially available chiral diamines and copper triflate proposed to self-assemble in conjunction with the chelating aldehydes, 4-substituted-2-picolinaldehydes or 4-methylthiazole-2-carboxaldehyde, to generate a catalyst complex. A model is provided to explain how this complex directs enantioselectivity. This work represents a significant advance in the ease, scope, and cost of producing highly substituted, enantioenriched pyrrolidines.

  11. Evaluation of injectable silica-embedded nanohydroxyapatite bone substitute in a rat tibia defect model

    Xu W

    2011-08-01

    Full Text Available Weiguo Xu1, Cornelia Ganz2, Ulf Weber2, Martin Adam2, Gerd Holzhüter2, Daniel Wolter3, Bernhard Frerich3, Brigitte Vollmar1, Thomas Gerber21Institute for Experimental Surgery, 2Institute of Physics, 3Department of Oral, Maxillofacial and Plastic Surgery, University of Rostock, Rostock, GermanyAbstract: In clinical practice, vertebral compression fractures occur after trauma and osteoporosis. Kyphoplasty is a minimally invasive procedure using bone filler material for the treatment of such fractures. A full synthetic injectable bone substitute (SIBS was manufactured by means of spray drying. The aim of this study was to characterize the SIBS and to analyze the remodelling process during degradation of the biomaterial and new bone formation after implantation. SIBS is an aqueous suspension of donut-like microparticles. These microparticles consist of nanocrystallites of synthetic hydroxyapatite embedded in amorphous silica gel. After implantation of SIBS in a proximal tibial diaphyseal defect in 52 rats, grafts were harvested for subsequent analysis on different days. Newly formed bone originating from endosteum was observed on day 6. Hematomas in the medullary space and cortical wounds disappeared on day 12. The wound region was completely replaced by a composite of newly formed cancellous bone, extracellular matrix, and SIBS. At day 63 the cortical defect was fully healed by bone, while newly formed bone in the medullary space almost disappeared and was replaced with bone marrow. In conclusion, SIBS demonstrated a unique structure with osteoinductive and bioresorbable properties, which induced fast bone regeneration. Therefore, a clinical application of SIBS for kyphoplasty is promising.Keywords: bone remodelling, electron microscopy, histomorphometry, nanotechnology, tissue engineering

  12. Substitution of carcinogenic solvent dichloromethane for the extraction of volatile compounds in a fat-free model food system.

    Cayot, Nathalie; Lafarge, Céline; Bou-Maroun, Elias; Cayot, Philippe

    2016-07-22

    Dichloromethane is known as a very efficient solvent, but, as other halogenated solvents, is recognized as a hazardous product (CMR substance). The objective of the present work is to propose substitution solvent for the extraction of volatile compounds. The most important physico-chemical parameters in the choice of an appropriate extraction solvent of volatile compounds are reviewed. Various solvents are selected on this basis and on their hazard characteristics. The selected solvents, safer than dichloromethane, are compared using the extraction efficiency of volatile compounds from a model food product able to interact with volatile compounds. Volatile compounds with different hydrophobicity are used. High extraction yields were positively correlated with high boiling points and high Log Kow values of volatile compounds. Mixtures of solvents such as azeotrope propan-2-one/cyclopentane, azeotrope ethyl acetate/ethanol, and mixture ethyl acetate/ethanol (3:1, v/v) gave higher extraction yields than those obtained with dichloromethane.

  13. EPR and optical studies of VO2+ doped potassium succinate-succinic acid single crystal - Substitutional incorporation

    Juliet sheela, K.; Radha Krishnan, S.; Shanmugam, V. M.; Subramanian, P.

    2017-03-01

    EPR and optical absorption studies of VO2+ doped potassium succinate-succinic acid (KSSA) single crystal has been examined at room temperature. EPR spectrum shows that well resolved hyperfine lines. The angular variation of the EPR spectra has shown that two different VO2+ complexes are located in different chemical environments. Among the number of sites, two sites have been followed and reported here. From the EPR analysis, spin Hamiltonian parameters g and A tensors and their directional cosines are evaluated. Both the sites experience rhombic crystal field symmetry around the impurity ion. The VO2+ ion entering the site location of potassium ion has coordination of eight oxygen atoms in a distorted dodecahedral arrangement. The Optical absorption spectrum studied at room temperature shows bands corresponding to C4v symmetry. The crystal field parameter and tetragonal field parameters are calculated. From the Optical and EPR data various molecular orbital coefficients are evaluated and the nature of bonding in the crystal is discussed.

  14. Comparison and preparation of multilayered polylactic acid fabric strengthen calcium phosphate-based bone substitutes for orthopedic applications.

    Chen, Wen-Cheng; Ko, Chia-Ling; Yang, Jia-Kai; Wu, Hui-Yu; Lin, Jia-Horng

    2016-03-01

    An attempt to maintain the three-dimensional space into restorative sites through the conveniently pack porous fillers are general used strategy. Advancement in the manufacturing protective shells in the scaffolds, which would be filled with brittle ceramic grafts for the development of highly connective pores provides the approach to solve crack problem for generating the tissues. Therefore, multilayered braided and alkalized poly(lactic acid) (PLA) composites with calcium phosphate bone cement (CPC) were synthesized and compared. The PLA/CPC composites were divided into various groups according to a series of heat-treatment temperatures (100-190 °C) and periods (1-3 h) and then characterized. The effects of 24-h immersion on the strength decay resistance of the samples were compared. Results showed that the residual oil capped on the surfaces of alkalized PLA braid was removed, and the structure was unaltered. However, the reduced tensile stress of alkalized PLA braids was due to ester-group formation by hydrolysis. Mechanical test results of PLA/CPC composites showed that the strength significantly increased after heat treatment, except when the heating temperature was higher than the PLA melting point at approximately 160-170 °C. The degree of PLA after recrystallization became higher than that of unheated composites, thereby leading to reduced strength and toughness of the specimen. Braiding fibers of biodegradable PLA reinforced and toughened the structure particularly of the extra-brittle material of thin-sheet CPC after implantation.

  15. Epsilon substituted lysinol derivatives as HIV-1 protease inhibitors.

    Jones, Kristen L G; Holloway, M Katharine; Su, Hua-Poo; Carroll, Steven S; Burlein, Christine; Touch, Sinoeun; DiStefano, Daniel J; Sanchez, Rosa I; Williams, Theresa M; Vacca, Joseph P; Coburn, Craig A

    2010-07-15

    A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors. Modeling studies and synthetic efforts suggest the potency increase is due to both conformational bias and van der Waals interactions with the S2 pocket.

  16. Substitution of aspartic acid for glycine at position 310 in type II collagen produces achondrogenesis II, and substitution of serine at position 805 produces hypochondrogenesis: analysis of genotype-phenotype relationships.

    Bonaventure, J; Cohen-Solal, L; Ritvaniemi, P; Van Maldergem, L; Kadhom, N; Delezoide, A L; Maroteaux, P; Prockop, D J; Ala-Kokko, L

    1995-01-01

    Two different mutations were found in two unrelated probands with lethal chondrodysplasias, one with achondrogenesis type II and the other with the less severe phenotype of hypochondrogenesis. The mutations in the COL2A1 gene were identified by denaturing gradient gel electrophoresis analysis of genomic DNA followed by dideoxynucleotide sequencing and restriction site analysis. The proband with achondrogenesis type II had a heterozygous single-base mutation that substituted aspartate for glycine at position 310 of the alpha 1(II) chain of type II procollagen. The proband with hypochondrogenesis had a heterozygous single-base mutation that substituted serine for glycine at position 805. Type II collagen extracted from cartilage from the probands demonstrated the presence of type I collagen and a delayed electrophoretic mobility, indicating post-translational overmodifications. Analysis of CNBr peptides showed that, in proband 1, the entire peptides were overmodified. Examination of chondrocytes cultured in agarose or alginate indicated that there was a delayed secretion of type II procollagen. In addition, type II collagen synthesized by cartilage fragments from the probands demonstrated a decreased thermal stability. The melting temperature of the type II collagen containing the aspartate-for-glycine substitution was reduced by 4 degrees C, and that of the collagen containing the serine-for-glycine substitution was reduced by 2 degrees C. Electron microscopy of the extracellular matrix from the chondrocyte cultures showed a decreased density of matrix and the presence of unusually short and thin fibrils. Our results indicate that glycine substitutions in the N-terminal region of the type II collagen molecule can produce more severe phenotypes than mutations in the C-terminal region. The aspartate-for-glycine substitution at position 310, which was associated with defective secretion and a probable increased degradation of collagen, is the most destabilizing

  17. Fluorine Substitution in Neurotransmitters: Microwave Spectroscopy and Modelling of the Conformational Space and Non Bonding Interactions

    Melandri, S.; Maris, A.; Merloni, A.

    2011-06-01

    Fluorine substitution in molecules is a common practice in bio-organic chemistry in order to modulate physicochemical properties and biological activity of molecules and an increasing number of drugs on the market contain fluorine, the presence of which is often of major importance to modify pharmacokinetics properties and molecular activity. The rationale for such a strategy is that fluorine is generally a stronger electron acceptor than the other halogen atoms and its size is intermediate between that of hydrogen and oxygen. We have studied two fluorinated analogs of 2-phenylethylamine (PEA), the prototype molecule for adrenergic neurotransmitters, namely: 4-Fluoro (4FPEA) and 2-Fluoro-2-phenylethylamine (2FPEA) by Molecular Beam Fourier Transform Microwave Spectroscopy in the frequency range 6-18 GHz and ab initio calculations at the MP2/6311++G** level. The aim is to obtain information on the spatial arrangement of the ethylamine side chain and the effects of fluorination on the energy landscape. The conformational space is dominated by low energy gauche conformations stabilized by weak interactions between the aminic hydrogens and the electron cloud of the benzene ring and anti conformations higher in energy. In 2FPEA the presence of the fluorine atom almost duplicate the number of possible conformation with respect to 4FPEA. We observed two conformers of 4FPEA and five conformers of 2FPEA which have been classified with the guide provided by accurate ab initio calculations. The identification of the conformational species was helped by the analysis of the quadrupole hyperfine pattern which is greatly influenced by the orientation of the amino group and acts as a fingerprint for each conformation. The orientation of the dipole moment within the principal axis frame and the order of stability of the different conformations are other independent pieces of evidence for the unambiguous assignment and identification of the conformers. The order of stability was

  18. Amino acid substitutions of conserved residues in the carboxyl-terminal domain of the [alpha]I(X) chain of type X collagen occur in two unrelated families with metaphyseal chondrodysplasia type Schmid

    Wallis, G.A.; Rash, B.; Sweetman, W.A.; Thomas, J.T.; Grant, M.E.; Boot-Handford, R.P. (Univ. of Manchester (United Kingdom)); Super, M. (Royal Manchester Children' s Hospital, Manchester (United Kingdom)); Evans, G. (Robert Jones Orthopaedic Hospital, Oswestry (United Kingdom))

    1994-02-01

    Type X collagen is a homotrimeric, short-chain, nonfibrillar extracellular-matrix component that is specifically and transiently synthesized by hypertrophic chondrocytes at the site of endochondral ossification. The precise function of type X collagen is not known, but its specific pattern of expression suggests that mutations within the encoding gene (COL10A1) that alter the structure or synthesis of the protein may cause heritable forms of chondrodysplasia. The authors used the PCR and the SSCP techniques to analyze the coding and upstream promoter regions of the COL10A1 gene in a number of individuals with forms of chondrodysplasia. Using this approach, they identified two individuals with metaphyseal chondrodysplasia type Schmid (MCDS) with SSCP changes in the region of the gene encoding the carboxyl-terminal domain. Sequence analysis demonstrated that the individuals were heterozygous for two unique single-base-pair transitions that led to the substitution of the highly conserved amino acid residue tyrosine at position 598 by aspartic acid in one person and of leucine at position 614 by proline in the other. The substitution at residue 598 segregated with the phenotype in a family of eight (five affected and three unaffected) related persons. The substitutions at residue 614 occurred in a sporadically affected individual but not in her unaffected mother and brother. Additional members of this family were not available for further study. These results suggest that certain amino acid substitutions within the carboxyl-terminal domain of the chains of the type X collagen molecule cause MCDS. These amino acid substitutions are likely to alter either chain recognition or assembly of the type X collagen molecule, thereby depleting the amount of normal type X collagen deposited in the extracellular matrix, with consequent aberrations in bone growth and development. 36 refs., 5 figs.

  19. Pharmacophore modeling and 3D-QSAR studies on substituted benzothiazole / benzimidazole analogues as DHFR inhibitors with antimycobacterial activity

    R. Priyadarsini

    2012-08-01

    Full Text Available The resurgence of tuberculosis and the emergence of multidrug-resistant strains of Mycobacteria drugs has propelled the development of new structural classes of antitubercular agents. The present study was undertaken to investigate the opportunities which the enzyme dihydrofolate reductase, a promising drug target for treatmentof Mycobacterial infections offers for the development of new TB drugs. Pharmacophore models were established by using the HipHop and HypoGen algorithms implemented in the Catalyst software package. Thebest quantitative pharmacophore model, consisted of two hydrogen bond acceptor, a hydrophobic aliphatic, and a ring aromatic feature which has the highest correlation coefficient (0.93, as well as enrichment factor of 1.75 and Goodness of hit score of 0.73. Based on the pharmacophore model some leads were optimized and some of its derivatives were synthesized and analysed by following QSAR studies. About 25 compounds of substituted benzothiazole/ benzimidazole derivatives were synthesized as potent DHFR inhibitors and screened for antimycobacterial activity. To further explore the structure-activity relationships of all newly synthesized compounds, 3D-QSAR analyses were developed. MFA studies were performed with the QSAR module of Cerius2 using genetic partial least squares (G/PLS algorithm. The predictive ability of the developed model was assessed using a training set of 25 and a test set of 5 compounds (r2pred = 0.924.The analyzed MF

  20. N-substituted benzyl matrinic acid derivatives inhibit hepatitis C virus (HCV replication through down-regulating host heat-stress cognate 70 (Hsc70 expression.

    Na-Na Du

    Full Text Available Heat-stress cognate 70 (Hsc70 is a host factor that helps hepatitis C virus (HCV to complete its life cycle in infected hepatocytes. Using Hsc70 as a target for HCV inhibition, a series of novel N-substituted benzyl matrinic/sophoridinic acid derivatives was synthesized and evaluated for their anti-HCV activity in vitro. Among these analogues, compound 7c possessing N-p-methylbenzyl afforded an appealing ability to inhibit HCV replication with SI value over 53. Furthermore, it showed a good oral pharmacokinetic profile with area-under-curve (AUC of 13.4 µM·h, and a considerably good safety in oral administration in mice (LD50>1000 mg/kg. As 7c suppresses HCV replication via an action mode distinctly different from that of the marketed anti-HCV drugs, it has been selected as a new mechanism anti-HCV candidate for further investigation, with an advantage of no or decreased chance to induce drug-resistant mutations.

  1. Currency Substitution in Turkey

    Ismail H. Genc

    2005-01-01

    Full Text Available We investigated whether the recent depreciations in the Turkish currency (Lira resulted in the currency substitution away from Lira by using quarterly data over the period from 1987:1 to 2000: 2 with M1 and M2 monetary aggregates and income, interest rate and exchange rate. Other than the variety of monetary aggregates, we tried different ways of including the interest rate into the models to ensure the robustness of our results. Our analysis shows that the currency substitution in fact happened with Lira.

  2. Evaluation of Osteoconductive and Osteogenic Potential of a Dentin-Based Bone Substitute Using a Calvarial Defect Model

    Ibrahim Hussain

    2012-01-01

    Full Text Available The aim of this study was to assess the osteoconductive and osteogenic properties of processed bovine dentin using a robust rabbit calvarial defect model. In total, 16 New Zealand White rabbits were operated to create three circular defects in the calvaria. One defect was left unfilled, one filled with collected autogenous bone, and the third defect was filled with the dentin-based bone substitute. Following surgery and after a healing period of either 1 or 6 weeks, a CT scan was obtained. Following sacrificing, the tissues were processed for histological examination. The CT data showed the density in the area grafted with the dentin-based material was higher than the surrounding bone and the areas grafted with autologous bone after 1 week and 6 weeks of healing. The area left unfilled remained an empty defect after 1 week and 6 weeks. Histological examination of the defects filled with the dentin product after 6 weeks showed soft tissue encapsulation around the dentin particles. It can be concluded that the rabbit calvarial model used in this study is a robust model for the assessment of bone materials. Bovine dentin is a biostable material; however, it may not be suitable for repairing large 4-wall defects.

  3. Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody

    Ng, Oi-Wing; Keng, Choong-Tat; Leung, Cynthia Sau-Wai; Peiris, J. S. Malik; Poon, Leo Lit Man; Tan, Yee-Joo

    2014-01-01

    The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) is the etiological agent for the infectious disease, SARS, which first emerged 10 years ago. SARS-CoV is a zoonotic virus that has crossed the species barriers to infect humans. Bats, which harbour a diverse pool of SARS-like CoVs (SL-CoVs), are believed to be the natural reservoir. The SARS-CoV surface Spike (S) protein is a major antigenic determinant in eliciting neutralizing antibody production during SARS-CoV infection. In our previous work, we showed that a panel of murine monoclonal antibodies (mAbs) that target the S2 subunit of the S protein are capable of neutralizing SARS-CoV infection in vitro (Lip KM et al, J Virol. 2006 Jan; 80(2): 941–50). In this study, we report our findings on the characterization of one of these mAbs, known as 1A9, which binds to the S protein at a novel epitope within the S2 subunit at amino acids 1111–1130. MAb 1A9 is a broadly neutralizing mAb that prevents viral entry mediated by the S proteins of human and civet SARS-CoVs as well as bat SL-CoVs. By generating mutant SARS-CoV that escapes the neutralization by mAb 1A9, the residue D1128 in S was found to be crucial for its interaction with mAb 1A9. S protein containing the substitution of D1128 with alanine (D1128A) exhibited a significant decrease in binding capability to mAb 1A9 compared to wild-type S protein. By using a pseudotyped viral entry assay, it was shown that the D1128A substitution in the escape virus allows it to overcome the viral entry blockage by mAb 1A9. In addition, the D1128A mutation was found to exert no effects on the S protein cell surface expression and incorporation into virion particles, suggesting that the escape virus retains the same viral entry property as the wild-type virus. PMID:25019613

  4. Substitution at aspartic acid 1128 in the SARS coronavirus spike glycoprotein mediates escape from a S2 domain-targeting neutralizing monoclonal antibody.

    Oi-Wing Ng

    Full Text Available The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV is the etiological agent for the infectious disease, SARS, which first emerged 10 years ago. SARS-CoV is a zoonotic virus that has crossed the species barriers to infect humans. Bats, which harbour a diverse pool of SARS-like CoVs (SL-CoVs, are believed to be the natural reservoir. The SARS-CoV surface Spike (S protein is a major antigenic determinant in eliciting neutralizing antibody production during SARS-CoV infection. In our previous work, we showed that a panel of murine monoclonal antibodies (mAbs that target the S2 subunit of the S protein are capable of neutralizing SARS-CoV infection in vitro (Lip KM et al, J Virol. 2006 Jan; 80(2: 941-50. In this study, we report our findings on the characterization of one of these mAbs, known as 1A9, which binds to the S protein at a novel epitope within the S2 subunit at amino acids 1111-1130. MAb 1A9 is a broadly neutralizing mAb that prevents viral entry mediated by the S proteins of human and civet SARS-CoVs as well as bat SL-CoVs. By generating mutant SARS-CoV that escapes the neutralization by mAb 1A9, the residue D1128 in S was found to be crucial for its interaction with mAb 1A9. S protein containing the substitution of D1128 with alanine (D1128A exhibited a significant decrease in binding capability to mAb 1A9 compared to wild-type S protein. By using a pseudotyped viral entry assay, it was shown that the D1128A substitution in the escape virus allows it to overcome the viral entry blockage by mAb 1A9. In addition, the D1128A mutation was found to exert no effects on the S protein cell surface expression and incorporation into virion particles, suggesting that the escape virus retains the same viral entry property as the wild-type virus.

  5. Design, Synthesis, and Crystal Structures of 6-Alkylidene-2 -Substituted Penicillanic Acid Sulfones as Potent Inhibitors of Acinetobacter baumannii OXA-24 Carbapenemase

    Bou, G.; Santillana, E; Sheri, A; Beceiro, A; Sampson, J; Kalp, M; Bethel, C; Distler, A; Drawz, S; et. al.

    2010-01-01

    Class D {beta}-lactamases represent a growing and diverse class of penicillin-inactivating enzymes that are usually resistant to commercial {beta}-lactamase inhibitors. As many such enzymes are found in multi-drug resistant (MDR) Acinetobacter baumannii and Pseudomonas aeruginosa, novel {beta}-lactamase inhibitors are urgently needed. Five unique 6-alkylidene-2{prime}-substituted penicillanic acid sulfones (1-5) were synthesized and tested against OXA-24, a clinically important {beta}-lactamase that inactivates carbapenems and is found in A. baumannii. Based upon the roles Tyr112 and Met223 play in the OXA-24 {beta}-lactamase, we also engineered two variants (Tyr112Ala and Tyr112Ala,Met223Ala) to test the hypothesis that the hydrophobic tunnel formed by these residues influences inhibitor recognition. IC{sub 50} values against OXA-24 and two OXA-24 {beta}-lactamase variants ranged from 10 {+-} 1 (4 vs WT) to 338 {+-} 20 nM (5 vs Tyr112Ala, Met223Ala). Compound 4 possessed the lowest K{sub i} (500 {+-} 80 nM vs WT), and 1 possessed the highest inactivation efficiency (k{sub inact}/K{sub i} = 0.21 {+-} 0.02 {micro}M{sup -1}s{sup -1}). Electrospray ionization mass spectrometry revealed a single covalent adduct, suggesting the formation of an acyl-enzyme intermediate. X-ray structures of OXA-24 complexed to four inhibitors (2.0-2.6 {angstrom}) reveal the formation of stable bicyclic aromatic intermediates with their carbonyl oxygen in the oxyanion hole. These data provide the first structural evidence that 6-alkylidene-2{prime}-substituted penicillin sulfones are effective mechanism-based inactivators of class D {beta}-lactamases. Their unique chemistry makes them developmental candidates. Mechanisms for class D hydrolysis and inhibition are discussed, and a pathway for the evolution of the BlaR1 sensor of Staphylococcus aureus to the class D {beta}-lactamases is proposed.

  6. Observation of the side chain O-methylation of glutamic acid or aspartic acid containing model peptides by electrospray ionization-mass spectrometry.

    Atik, A Emin; Guray, Melda Z; Yalcin, Talat

    2017-03-15

    O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC-MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions.

  7. MODELLING THE INHIBITORY ACTIVITY ON CARBONIC ANHYDRASE IV OF SUBSTITUTED THIADIAZOLE - AND THIADIAZOLINE - DISULFONAMIDES: INTEGRATION OF STRUCTURE INFORMATION

    Sorana Daniela Bolboaca

    2006-07-01

    Full Text Available ABSTRACT:Purpose: To analyze the relationships between inhibitory activities on carbonic anhydrase IV and structures of substituted 1,3,4-thiadiazole and 1,3,4-thiadiazoline disulfonamide through integration of compounds complex structure information by the use of Molecular Descriptors Family.Method: A number of forty compounds were used to generate and compute the molecular descriptors family and to build structure-activity relationships models. The obtained multi-varied models (the models with two, respectively with four descriptors were validated by computing the cross-validation leave-one-out score (r2cv-loo, and analyzed through assessment of the squared correlation coefficients (r2, and the models stability (r2 - r2cv-loo. The estimation abilities of the multi-varied MDF-SAR model with four descriptors were analyzed in training and test sets.Results: Analysis of the obtained models shows that the best results was obtained by the multi-varied model with four molecular descriptors (r2 = 0.920. The prediction abilities of this model is sustained by the cross validation leave-one-out score (r2cv-loo = 0.903, the model stability (r2 - r2cv-loo = 0.017, and the results on training versus test analysis (no significant differences between correlation coefficients in training and test sets, p > 0.05. The multi-varied model which used four descriptors proved to render higher value of correlation coefficient comparing with previous reported models (p 0.05. El modelo multivariante que utilizó cuatro descriptores mostró un valor más alto del coeficiente de correlación en comparación con los modelos divulgados anteriormente (p < 0.01.Conclusión: El modelo multivariante con cuatro descriptores es sólido y fiable e indica que la actividad de la inhibición en la carboanhidrasa IV producida por las sufonamidas sustituidas del 1,3,4-tiadiazol- y de la 1,3,4-tiadiazolina- dependen de la naturaleza de la geometría y de la topología del compuesto

  8. On the mechanical characterization and modeling of polymer gel brain substitute under dynamic rotational loading.

    Fontenier, B; Hault-Dubrulle, A; Drazetic, P; Fontaine, C; Naceur, H

    2016-10-01

    The use of highly sensitive soft materials has become increasingly apparent in the last few years in numerous industrial fields, due to their viscous and damping nature. Unfortunately these materials remain difficult to characterize using conventional techniques, mainly because of the very low internal forces supported by these materials especially under high strain-rates of deformation. The aim of this work is to investigate the dynamic response of a polymer gel brain analog material under specific rotational-impact experiments. The selected polymer gel commercially known as Sylgard 527 has been studied using a specific procedure for its experimental characterization and numerical modeling. At first an indentation experiment was conducted at several loading rates to study the strain rate sensitivity of the Sylgard 527 gel. During the unloading several relaxation tests were performed after indentation, to assess the viscous behavior of the material. A specific numerical procedure based on moving least square approximation and response surface method was then performed to determine adequate robust material parameters of the Sylgard 527 gel. A sensitivity analysis was assessed to confirm the robustness of the obtained material parameters. For the validation of the obtained material model, a second experiment was conducted using a dynamic rotational loading apparatus. It consists of a metallic cylindrical cup filled with the polymer gel and subjected to an eccentric transient rotational impact. Complete kinematics of the cup and the large strains induced in the Sylgard 527 gel, have been recorded at several patterns by means of optical measurement. The whole apparatus was modeled by the Finite Element Method using explicit dynamic time integration available within Ls-dyna(®) software. Comparison between the physical and the numerical models of the Sylgard 527 gel behavior under rotational choc shows excellent agreements.

  9. Axial vascularization of a large volume calcium phosphate ceramic bone substitute in the sheep AV loop model.

    Beier, Justus P; Horch, Raymund E; Hess, Andreas; Arkudas, Andreas; Heinrich, Johanna; Loew, Johanna; Gulle, Heinz; Polykandriotis, Elias; Bleiziffer, Oliver; Kneser, Ulrich

    2010-03-01

    Vascularization still remains an obstacle to engineering of bone tissue with clinically relevant dimensions. Our aim was to induce axial vascularization in a large volume of a clinically approved biphasic calcium phosphate ceramic by transferring the arteriovenous (AV) loop approach to a large animal model. HA/beta-TCP granula were mixed with fibrin gel for a total volume of 16 cm(3), followed by incorporation into an isolation chamber together with an AV loop. The chambers were implanted into the groins of merino sheep and the development of vascularization was monitored by sequential non-invasive magnetic resonance imaging (MRI). The chambers were explanted after 6 and 12 weeks, the pedicle was perfused with contrast agent and specimens were subjected to micro-computed tomography (micro-CT) scan and histological analysis. Sequential MRI demonstrated a significantly increased perfusion in the HA/beta-TCP matrices over time. Micro-CT scans and histology confirmed successful axial vascularization of HA/beta-TCP constructs. This study demonstrates, for the first time, successful axial vascularization of a clinically approved bone substitute with a significant volume in a large animal model by means of a microsurgically created AV loop, thus paving the way for the first microsurgical transplantation of a tissue-engineered, axially vascularized bone with clinically relevant dimensions.

  10. THE IDEA OF CREATING DOMESTIC SOFTWARE COMPLEX OF DIGITAL GRAPHIC MODELING IN THE CONTEXT OF IMPORT SUBSTITUTION STRATEGY

    V. V. MIROSHNIKOV

    2015-01-01

    Full Text Available The article focuses on the problem of import substitution in the field of IT-technologies, in particular, the practice of visual modeling in the process of designing the objects of architecture and design. The author presents the idea of creating national multifunctional software complex for visual modeling as a topical alternative to foreign analogues. The topicality of the ideas is determined by several factors: the increased risks for the technological sovereignty of the country, the need to optimize the practice of designing the objects of architecture and design, rapid development of domestic industry of IT-technologies. The article describes in detail the proposal for the creation of software based on the latest IT- technologies, maximum optimized in terms of interoperability through its constituent units, taking into consideration the eculiarities of mentality and language culture and traditions of local users and the specifics of the algorithms of design process. The idea set forth in the article aims to familiarize practitioners of design and architecture with options for addressing the urgent, in the author‟s opinion, complex problem in the field of digital modeling in various areas of design practice and information exchange. The author‟s suggestions are based on his own practical experience of project modeling and teaching professional designers.

  11. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of -alkyl substitution on regioselectivity and reaction rate

    Mallayan Palaniandavar; Kusalendiran Visvaganesan

    2011-03-01

    Catechol dioxygenases are responsible for the last step in the biodegradation of aromatic molecules in the environment. The iron(II) active site in the extradiol-cleaving enzymes cleaves the C-C bond adjacent to the hydroxyl group, while the iron(III) active site in the intradiol-cleaving enzymes cleaves the C-C bond in between two hydroxyl groups. A series of mononuclear iron(III) complexes of the type [Fe(L)Cl3], where L is the linear -alkyl substituted bis(pyrid-2-ylmethyl)amine, -alkyl substituted -(pyrid-2-ylmethyl)ethylenediamine, linear tridentate 3N ligands containing imidazolyl moieties and tripodal ligands containing pyrazolyl moieties have been isolated and studied as structural and functional models for catechol dioxygenase enzymes. All the complexes catalyse the cleavage of catechols using molecular oxygen to afford both intra- and extradiol cleavage products. The rate of oxygenation depends on the solvent and the Lewis acidity of iron(III) center as modified by the sterically demanding -alkyl groups. Also, our studies reveal that stereo-electronic factors like the Lewis acidity of the iron(III) center and the steric demand of ligands, as regulated by the -alkyl substituents, determine the regioselectivity and the rate of dioxygenation. In sharp contrast to all these complexes, the pyrazole-containing tripodal ligand complexes yield mainly the oxidized product benzoquinone.

  12. Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance.

    Yu, Qin; Jalaludin, Adam; Han, Heping; Chen, Ming; Sammons, R Douglas; Powles, Stephen B

    2015-04-01

    Glyphosate is the most important and widely used herbicide in world agriculture. Intensive glyphosate selection has resulted in the widespread evolution of glyphosate-resistant weed populations, threatening the sustainability of this valuable once-in-a-century agrochemical. Field-evolved glyphosate resistance due to known resistance mechanisms is generally low to modest. Here, working with a highly glyphosate-resistant Eleusine indica population, we identified a double amino acid substitution (T102I+P106S [TIPS]) in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant individuals. This TIPS mutation recreates the biotechnology-engineered commercial first generation glyphosate-tolerant EPSPS in corn (Zea mays) and now in other crops. In E. indica, the naturally evolved TIPS mutants are highly (more than 180-fold) resistant to glyphosate compared with the wild type and more resistant (more than 32-fold) than the previously known P106S mutants. The E. indica TIPS EPSPS showed very high-level (2,647-fold) in vitro resistance to glyphosate relative to the wild type and is more resistant (600-fold) than the P106S variant. The evolution of the TIPS mutation in crop fields under glyphosate selection is likely a sequential event, with the P106S mutation being selected first and fixed, followed by the T102I mutation to create the highly resistant TIPS EPSPS. The sequential evolution of the TIPS mutation endowing high-level glyphosate resistance is an important mechanism by which plants adapt to intense herbicide selection and a dramatic example of evolution in action.

  13. Amino acid substitutions in HIV-1 reverse transcriptase with corresponding residues from HIV-2. Effect on kinetic constants and inhibition by non-nucleoside analogs.

    Bacolla, A; Shih, C K; Rose, J M; Piras, G; Warren, T C; Grygon, C A; Ingraham, R H; Cousins, R C; Greenwood, D J; Richman, D

    1993-08-05

    Nevirapine is a highly potent and specific inhibitor of human immunodeficiency virus type 1 (HIV-1) polymerase, but is inactive against HIV-2 and other polymerase. Previous studies demonstrated that residues 176-190 of HIV-1 reverse transcriptase (RT) can confer nevirapine sensitivity to HIV-2 RT. To better characterize the role of this sequence in HIV-1 RT, we have progressively substituted residues 176-190 of HIV-2 RT for those of HIV-1 RT and monitored the impact on the kinetic properties; inhibitory activity of nevirapine (11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[2,3-b:2',3'-e] [1,4]diazepin-6-one), E-BPU (5-ethyl-1-benzyloxymethyl-6-(phenylthio)-uracil), and TIBO-R82150 ((+)-S-4,5,6,7-tetrahydro-5-methyl-6-(3-methyl-2-butenyl)imidazo[4,5,1-j k] [1,4]benzodiazepin-2(1H)-thione); and inhibitor-induced fluorescence changes of the mutant enzymes. The study revealed that in addition to Try-181 and Tyr-188, a new amino acid residue (Gly-190) plays an important role in determining susceptibility to nevirapine and E-BPU, but not to TIBO-R82150. These data argue that these non-nucleoside inhibitors fit differently, even though they share a common binding pocket. Nevirapine was seen to exert inhibitory activity by altering the interaction of the enzyme with the template-primer. Kinetic parameters were modulated by the template (DNA versus RNA) as well as by some of the mutations.

  14. A smoothing expectation and substitution algorithm for the semiparametric accelerated failure time frailty model.

    Johnson, Lynn M; Strawderman, Robert L

    2012-09-20

    This paper proposes an estimation procedure for the semiparametric accelerated failure time frailty model that combines smoothing with an Expectation and Maximization-like algorithm for estimating equations. The resulting algorithm permits simultaneous estimation of the regression parameter, the baseline cumulative hazard, and the parameter indexing a general frailty distribution. We develop novel moment-based estimators for the frailty parameter, including a generalized method of moments estimator. Standard error estimates for all parameters are easily obtained using a randomly weighted bootstrap procedure. For the commonly used gamma frailty distribution, the proposed algorithm is very easy to implement using widely available numerical methods. Simulation results demonstrate that the algorithm performs very well in this setting. We re-analyz several previously analyzed data sets for illustrative purposes.

  15. The evolutionary appearance of non-cyanogenic hydroxynitrile glucosides in the Lotus genus is accompanied by the substrate specialization of paralogous β-glucosidases resulting from a crucial amino acid substitution.

    Lai, Daniela; Abou Hachem, Maher; Robson, Fran; Olsen, Carl Erik; Wang, Trevor L; Møller, Birger L; Takos, Adam M; Rook, Fred

    2014-07-01

    Lotus japonicus, like several other legumes, biosynthesizes the cyanogenic α-hydroxynitrile glucosides lotaustralin and linamarin. Upon tissue disruption these compounds are hydrolysed by a specific β-glucosidase, resulting in the release of hydrogen cyanide. Lotus japonicus also produces the non-cyanogenic γ- and β-hydroxynitrile glucosides rhodiocyanoside A and D using a biosynthetic pathway that branches off from lotaustralin biosynthesis. We previously established that BGD2 is the only β-glucosidase responsible for cyanogenesis in leaves. Here we show that the paralogous BGD4 has the dominant physiological role in rhodiocyanoside degradation. Structural modelling, site-directed mutagenesis and activity assays establish that a glycine residue (G211) in the aglycone binding site of BGD2 is essential for its ability to hydrolyse the endogenous cyanogenic glucosides. The corresponding valine (V211) in BGD4 narrows the active site pocket, resulting in the exclusion of non-flat substrates such as lotaustralin and linamarin, but not of the more planar rhodiocyanosides. Rhodiocyanosides and the BGD4 gene only occur in L. japonicus and a few closely related species associated with the Lotus corniculatus clade within the Lotus genus. This suggests the evolutionary scenario that substrate specialization for rhodiocyanosides evolved from a promiscuous activity of a progenitor cyanogenic β-glucosidase, resembling BGD2, and required no more than a single amino acid substitution.

  16. A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture.

    Liu, Yi; Holte, Sarah; Rao, Ushnal; McClure, Jan; Konopa, Philip; Swain, J Victor; Lanxon-Cookson, Erinn; Kim, Moon; Chen, Lennie; Mullins, James I

    2013-04-01

    Fixation of mutations in human immunodeficiency virus type 1 (HIV-1), such as those conferring drug resistance and immune escape, can result in a change in replication fitness. To assess these changes, a real-time TaqMan PCR detection assay and statistical methods for data analysis were developed to estimate sensitively relative viral fitness in competitive viral replication experiments in cell culture. Chimeric viruses with the gene of interest in an HIV-1NL4-3 backbone were constructed in two forms, vifA (native vif gene in NL4-3) and vifB (vif gene with six synonymous nucleotide differences from vifA). Subsequently, mutations of interest were introduced into the chimeric viruses in NL4-3VifA backbones, and the mutants were competed against the chimera with the isogenic viral sequence in the NL4-3VifB backbone in cell culture. In order to assess subtle fitness differences, culture supernatants were sampled longitudinally, and the viruses differentially quantified using vifA- and vifB-specific primers in real-time PCR assays. Based on an exponential net growth model, the growth rate of each virus was determined and the fitness cost of the mutation(s) distinguishing the two viruses represented as the net growth rate difference between the mutant and the native variants. Using this assay, the fitness impact of eight amino acid substitutions was quantitated at highly conserved sites in HIV-1 Gag and Env.

  17. Perfluorooctanoic acid rigidifies a model lipid membrane

    Brüning, B.A.; Farago, B.

    2014-01-01

    We report a combined dynamic light scattering and neutron spin-echo (NSE) study on vesicles composed of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine under the influence of varying amounts of perfluorooctanoic acid. We study local lipid bilayer undulations using NSE on time scale

  18. Effect of Isotopic Substitution on Elementary Processes in Dye-Sensitized Solar Cells: Deuterated Amino-Phenyl Acid Dyes on TiO2

    Sergei Manzhos

    2013-03-01

    Full Text Available We present the first computational study of the effects of isotopic substitution on the operation of dye-sensitized solar cells. Ab initio molecular dynamics is used to study the effect of deuteration on light absorption, dye adsorption dynamics, the averaged over vibrations driving force to injection (∆Gi and regeneration (∆Gr, as well as on promotion of electron back-donation in dyes NK1 (2E,4E-2-cyano-5-(4-dimethylaminophenylpenta-2,4-dienoic acid and NK7 (2E,4E-2-cyano-5-(4-diphenylaminophenylpenta-2,4-dienoic acid adsorbed in monodentate molecular and bidentate bridging dissociative configurations on the anatase (101 surface of TiO2. Deuteration causes a red shift of the absorption spectrum of the dye/TiO2 complex by about 5% (dozens of nm, which can noticeably affect the overlap with the solar spectrum in real cells. The dynamics effect on the driving force to injection and recombination (the difference between the averaged <∆Gi,r> and ∆Gi,requil at the equilibrium configuration is strong, yet there is surprisingly little isotopic effect: the average driving force to injection <∆Gi> and to regeneration <∆Gr> changes by only about 10 meV upon deuteration. The nuclear dynamics enhance recombination to the dye ground state due to the approach of the electron-donating group to TiO2, yet this effect is similar for deuterated and non-deuterated dyes. We conclude that the nuclear dynamics of the C-H(D bonds, mostly affected by deuteration, might not be important for the operation of photoelectrochemical cells based on organic dyes. As the expectation value of the ground state energy is higher than its optimum geometry value (by up to 0.1 eV in the present case, nuclear motions will affect dye regeneration by recently proposed redox shuttle-dye combinations operating at low driving forces.

  19. Expression and functional characterization of the Agrobacterium VirB2 amino acid substitution variants in T-pilus biogenesis, virulence, and transient transformation efficiency.

    Hung-Yi Wu

    Full Text Available Agrobacterium tumefaciens is a phytopathogenic bacterium that causes crown gall disease by transferring transferred DNA (T-DNA into the plant genome. The translocation process is mediated by the type IV secretion system (T4SS consisting of the VirD4 coupling protein and 11 VirB proteins (VirB1 to VirB11. All VirB proteins are required for the production of T-pilus, which consists of processed VirB2 (T-pilin and VirB5 as major and minor subunits, respectively. VirB2 is an essential component of T4SS, but the roles of VirB2 and the assembled T-pilus in Agrobacterium virulence and the T-DNA transfer process remain unknown. Here, we generated 34 VirB2 amino acid substitution variants to study the functions of VirB2 involved in VirB2 stability, extracellular VirB2/T-pilus production and virulence of A. tumefaciens. From the capacity for extracellular VirB2 production (ExB2+ or ExB2- and tumorigenesis on tomato stems (Vir+ or Vir-, the mutants could be classified into three groups: ExB2-/Vir-, ExB2-/Vir+, and ExB2+/Vir+. We also confirmed by electron microscopy that five ExB2-/Vir+ mutants exhibited a wild-type level of virulence with their deficiency in T-pilus formation. Interestingly, although the five T-pilus-/Vir+ uncoupling mutants retained a wild-type level of tumorigenesis efficiency on tomato stems and/or potato tuber discs, their transient transformation efficiency in Arabidopsis seedlings was highly attenuated. In conclusion, we have provided evidence for a role of T-pilus in Agrobacterium transformation process and have identified the domains and amino acid residues critical for VirB2 stability, T-pilus biogenesis, tumorigenesis, and transient transformation efficiency.

  20. Coralline hydroxyapatite is a suitable bone graft substitute in an intra-articular goat defect model.

    Koëter, S; Tigchelaar, S J; Farla, P; Driessen, L; van Kampen, A; Buma, P

    2009-07-01

    Intra-articular defects can be filled with an autologous bone graft taken from the iliac crest. This can be indicated after trauma or following correcting osteotomy. Patients may encounter donor site morbidity after this procedure. In this in vivo study, we studied if coralline hydroxyapatite (CHA) is a suitable material to replace autologous bone graft to fill a defect in the femoral trochlea of goats. CHA did not evoke any negative reaction in the synovium, and the articular cartilage was comparable to controls. In the bone graft group, we found scattered areas of (enchondral formed) bone. Most bone graft had been resorbed or remodeled, and the scarce remnants were incorporated into new bone. Resorption of CHA was limited or absent and most CHA was surrounded by new bone. In areas with fragmented CHA, close to the joint surface, numerous giant cells were found. The study shows that in this animal model, CHA inserted in a defect that directly communicates with the joint space incorporates into bone. This study did not show any negative effects of CHA in a joint environment.

  1. Modeling of Efficient Hot Air Drying of Apple Snails (Pomacea canaliculata for Use as a Fishmeal Protein Substitute

    Du Luo

    2015-05-01

    Full Text Available Snails are a kind of important aquatic products and dehydration is the main technique in production of snail meal. Apple snail (Pomacea canaliculata dehydration meets both the demand for a fishmeal substitute in aquaculture and invasive species control in agriculture. In this study, we investigated the percentage of the nutritive material, examined the drying characteristics at 60, 80, 100 and 120°C, respectively, established a drying kinetics model and explored the effect of body morphology on drying efficiency. The results showed that the wet weight percentage of the soft parts was 46.61±6.18%. The drying efficiency was significantly improved with an increase of drying temperature from 60 to 120°C. The drying time increased rapidly when the final moisture content approached its equilibrium value. The Hii et al. model was selected as the best model to describe the drying curves (R2>0.99. It provided a relatively accurate prediction between the requirements of moisture content and drying time. There were statistically significant differences (p<0.01 in the drying time at 10.0 and 1.0% moisture content level among the four temperature groups. The drying efficiency was significantly correlated to the mass of the soft parts. It was found that 100°C was an appropriate temperature to effectively dehydrate the fresh apple snails, whereas 60°C was not suitable when air velocity ≤0.5 m/s. This study explored an integrated approach to efficiently dehydrate snails for snail meal production, which will benefit both aquaculture and agriculture.

  2. Exact Wave Packet Dynamics of Singlet Fission in Unsubstituted and Substituted Polyene Chains within Long-Range Interacting Models

    Prodhan, Suryoday

    2016-01-01

    Singlet fission is a potential pathway for significant enhancement of efficiency in organic solar cells. In this article, we have studied singlet fission in a pair of polyene molecules employing exact many-body wave packet dynamics. The individual molecules are treated within Hubbard and Pariser-Parr-Pople (PPP) models and the interaction between them involves transfer terms, intersite electron repulsions and site charge-bond charge repulsion terms. Initial wave packet is constructed from excited singlet state of one molecule and ground state of the other. Time development of this wave packet under the influence of intermolecular interactions is followed within the Schr\\"{o}dinger picture by an efficient predictor-corrector scheme. In unsubstituted Hubbard and PPP chains, $2{}^1A$ excited singlet state leads to significant fission yield while the $1{}^1B$ state gives negligible fission yield. On substitution by donor-acceptor groups of moderate strength, singlet state derived from $1{}^1B$ state also gives si...

  3. Supramolecular complex formation of β-cyclodextrin polymer with substituted salicylic acid or 3-hydroxy-2-naphthoic acid and their electrorheological behaviors

    GAO; Ziwei; ZHAO; Xiaopeng; SUN; Ping; SI; Gang

    2004-01-01

    supramolecular systems (XXXV) --Synthesis of novel β-cyclodextrin derivative beating pyridinio group and its chiral discrimination of amino acids, Science in China, Ser. B, 2001, 44(3): 260-267.[13]Liu, Y., Yang, Y. W., Cao, R. et al., Thermodynamic origin of molecular selective binding of bile salts by aminated β-cyclodextrins,J. Phys. Chem. B, 2003: 14130-14139.[14]Liu, Y., Chen, G. S., Li, L. et al., Inclusion complexation and solubilization of paclitaxel by bridged bis(β-cyclodextrin)s containing a tetraethylenepentaamino spacer, J. Med. Chem., 2003,46(22): 4634-4637.[15]Yoshida, K., Shimomura, T., Ito, K. et al., Inclusion complex formation of cyclodextrin and polyaniline, Langmuir, 1999, 15(4):910-913.[16]Crini, G., Bertini, S., Torri, G. et al., Sorption of aromatic co-pounds in water using insoluble cyclodextrin polymers, J.Appllied Polymer Science, 1998, 68: 1973-1978.[17]Renard, E., Deratani, A., Volet, G. et al., Preparation and characterization of water soluble high molecular weight β-cyclodextrinepichlorohydrin polymers, Eur. Polym. J., 1997, 33(1): 49-57.[18]Gao, Z. W., Zhao, X. P., Electrorheological properties of inclusive complex of β-cyclodextrin polymer, Materials Letters, 2002, 57:615-618.[19]Gao, Z. W., Zhao, X. P., Enhancing electrorheological behaviors with formation of β-cyclodextrin supramolecular complex, Polymer, 2003, 44:4519-4526.[20]Su, X. D., Liu, L. Z., Shen, H. Y., Study on the absorbing enrichment of trace metals using α-pyridylaxo-β-naphthol inclusion complexes of cyclodextrin polymer resin, Analytical Chemistry (in Chinese), 1995, 23(12): 1361-1366.[21]Catena, G. C., Bright, F. V., Thermodynamic study on the effects of β-cyclodextrin inclusion with anilinonaphthalenesulfonates,Anal. Chem., 1989, 61: 905-909.[22]Kano, K., Tatsumi, M., Hashimoto, S., Cyclodextrin-induced conformational enantiomerism of dinaphthylmethanes, J. Org.Chem., 1991, 56: 6579-6585.

  4. Coordinate induction of hepatic fatty acyl-CoA oxidase and P4504A1 in rat after activation of the peroxisome proliferator-activated receptor (PPAR) by sulphur-substituted fatty acid analogues.

    Demoz, A; Vaagenes, H; Aarsaether, N; Hvattum, E; Skorve, J; Göttlicher, M; Lillehaug, J R; Gibson, G G; Gustafsson, J A; Hood, S

    1994-09-01

    1. In the liver of rat fed a single dose of 3-thia fatty acids, 3-dithiahexadecanedioic acid (3-thiadicarboxylic acid) and tetradecylthioacetic acid, steady-state levels of P4504A1 and fatty acyl-CoA oxidase mRNAs increased in parallel. The increases were significant 8 h after administration, reaching a maximum after 12 h and decreased from 12 to 24 h after administration. 2. The corresponding enzyme activities of P4504A1 and fatty acyl-CoA oxidase were also induced in a parallel manner by the 3-thia fatty acids. The enzyme activities were significantly increased 12 h after administration and increased further after 24 h. This may reflect a possible effect of the 3-thia fatty acids not only on mRNA levels, but also on the translation and degradation rate of the two enzymes. 3. Repeated administration of 3-thia fatty acids resulted in an increase of the specific P4504A1 protein accompanied with an increased lauric acid hydroxylase activity. The correlation between induction of P4504A1 and fatty acyl-CoA oxidase mRNAs and their enzyme activities may reflect a coordinated rather than a causative induction mechanism, and that these genes respond to a common signal. This suggests that the increased P450 activity may not be responsible or be a prerequisite for fatty acyl-CoA oxidase induction. 4. Since the peroxisome proliferator-activated receptor (PPAR) plays a role in mediating the induction of fatty acyl-CoA oxidase, we analysed the activation of PPAR by fatty acids and sulphur-substituted analogues utilizing a chimera between the N-terminal and DNA-binding domain of the glucocorticoid receptor and the putative ligand-binding domain of PPAR. Arachidonic acid activated this chimeric receptor in Chinese hamster ovary cells. Inhibitors of P450 did not affect the activation of PPAR by arachidonic acid. Furthermore, dicarboxylic acids including 1,12-dodecanedioic acid or 1,16-hexadecanedioic acid only weakly activated the chimera. 3-Thidicarboxylic acid, however, was a

  5. A single amino acid substitution in IIIf subfamily of basic helix-loop-helix transcription factor AtMYC1 leads to trichome and root hair patterning defects by abolishing its interaction with partner proteins in Arabidopsis.

    Zhao, Hongtao; Wang, Xiaoxue; Zhu, Dandan; Cui, Sujuan; Li, Xia; Cao, Ying; Ma, Ligeng

    2012-04-20

    Plant trichomes and root hairs are powerful models for the study of cell fate determination. In Arabidopsis thaliana, trichome and root hair initiation requires a combination of three groups of proteins, including the WD40 repeat protein transparent TESTA GLABRA1 (TTG1), R2R3 repeat MYB protein GLABRA1 (GL1), or werewolf (WER) and the IIIf subfamily of basic helix-loop-helix (bHLH) protein GLABRA3 (GL3) or enhancer of GLABRA3 (EGL3). The bHLH component acts as a docking site for TTG1 and MYB proteins. Here, we isolated a mutant showing defects in trichome and root hair patterning that carried a point mutation (R173H) in AtMYC1 that encodes the fourth member of IIIf bHLH family protein. Genetic analysis revealed partial redundant yet distinct function between AtMYC1 and GL3/EGL3. GLABRA2 (GL2), an important transcription factor involved in trichome and root hair control, was down-regulated in Atmyc1 plants, suggesting the requirement of AtMYC1 for appropriate GL2 transcription. Like its homologs, AtMYC1 formed a complex with TTG1 and MYB proteins but did not dimerized. In addition, the interaction of AtMYC1 with MYB proteins and TTG1 was abrogated by the R173H substitution in Atmyc1-1. We found that this amino acid (Arg) is conserved in the AtMYC1 homologs GL3/EGL3 and that it is essential for their interaction with MYB proteins and for their proper functions. Our findings indicate that AtMYC1 is an important regulator of trichome and root hair initiation, and they reveal a novel amino acid necessary for protein-protein interactions and gene function in IIIf subfamily bHLH transcription factors.

  6. Capillary microreactors for lactic acid extraction: experimental and modelling study

    Susanti, Susanti; Winkelman, Jozef; Schuur, Boelo; Heeres, Hero; Yue, Jun

    2015-01-01

    Lactic acid is an important biobased chemical and, among others, is used for the production of poly-lactic acid. Down-stream processing using state of the art technology is energy intensive and leads to the formation of large amounts of salts. In this presentation, experimental and modeling studies

  7. Palladium-Catalyzed Asymmetric Conjugate Addition of Arylboronic Acids to Five-, Six-, and Seven-Membered β-Substituted Cyclic Enones: Enantioselective Construction of All-Carbon Quaternary Stereocenters

    Kikushima, Kotaro

    2011-05-11

    The first enantioselective Pd-catalyzed construction of all-carbon quaternary stereocenters via 1,4-addition of arylboronic acids to β-substituted cyclic enones is reported. Reaction of a wide range of arylboronic acids and cyclic enones using a catalyst prepared from Pd(OCOCF(3))(2) and a chiral pyridinooxazoline ligand yields enantioenriched products bearing benzylic stereocenters. Notably, this transformation is tolerant to air and moisture, providing a practical and operationally simple method of synthesizing enantioenriched all-carbon quaternary stereocenters.

  8. Gas-grain Modeling of Isocyanic Acid (HNCO), Cyanic Acid (HOCN), Fulminic Acid (HCNO), and Isofulminic Acid (HONC) in Assorted Interstellar Environments

    Quan, Donghui; Herbst, Eric; Osamura, Yoshihiro; Roueff, Evelyne

    2010-12-01

    Isocyanic acid (HNCO) is a well-known interstellar molecule. Evidence also exists for the presence of two of its metastable isomers in the interstellar medium: HCNO (fulminic acid) and HOCN (cyanic acid). Fulminic acid has been detected toward cold and lukewarm sources, while cyanic acid has been detected both in these sources and in warm sources in the Galactic Center. Gas-phase models can reproduce the abundances of the isomers in cold sources, but overproduce HCNO in the Galactic Center. Here we present a detailed study of a gas-grain model that contains these three isomers, plus a fourth isomer, isofulminic acid (HONC), for four types of sources: hot cores, the warm envelopes of hot cores, lukewarm corinos, and cold cores. The current model is partially able to rationalize the abundances of HNCO, HOCN, and HCNO in cold and warm sources. Predictions for HONC in all environments are also made.

  9. Structural Equation Modeling for Analyzing Erythrocyte Fatty Acids in Framingham

    James V. Pottala

    2014-01-01

    Full Text Available Research has shown that several types of erythrocyte fatty acids (i.e., omega-3, omega-6, and trans are associated with risk for cardiovascular diseases. However, there are complex metabolic and dietary relations among fatty acids, which induce correlations that are typically ignored when using them as risk predictors. A latent variable approach could summarize these complex relations into a few latent variable scores for use in statistical models. Twenty-two red blood cell (RBC fatty acids were measured in Framingham (N = 3196. The correlation matrix of the fatty acids was modeled using structural equation modeling; the model was tested for goodness-of-fit and gender invariance. Thirteen fatty acids were summarized by three latent variables, and gender invariance was rejected so separate models were developed for men and women. A score was developed for the polyunsaturated fatty acid (PUFA latent variable, which explained about 30% of the variance in the data. The PUFA score included loadings in opposing directions among three omega-3 and three omega-6 fatty acids, and incorporated the biosynthetic and dietary relations among them. Whether the PUFA factor score can improve the performance of risk prediction in cardiovascular diseases remains to be tested.

  10. Theoretical modeling of iodine value and saponification value of biodiesel fuels from their fatty acid composition

    Gopinath, A.; Puhan, Sukumar; Nagarajan, G. [Internal Combustion Engineering Division, Department of Mechanical Engineering, Anna University, Chennai 600 025, Tamil Nadu (India)

    2009-07-15

    Biodiesel is an alternative fuel consisting of alkyl esters of fatty acids from vegetable oils or animal fats. The properties of biodiesel depend on the type of vegetable oil used for the transesterification process. The objective of the present work is to theoretically predict the iodine value and the saponification value of different biodiesels from their fatty acid methyl ester composition. The fatty acid ester compositions and the above values of different biodiesels were taken from the available published data. A multiple linear regression model was developed to predict the iodine value and saponification value of different biodiesels. The predicted results showed that the prediction errors were less than 3.4% compared to the available published data. The predicted values were also verified by substituting in the available published model which was developed to predict the higher heating values of biodiesel fuels from their iodine value and the saponification value. The resulting heating values of biodiesels were then compared with the published heating values and reported. (author)

  11. Concentration Boundary Layer Model of Mortar Corrosion by Sulfuric Acid

    SONG Zhigang; ZHANG Xuesong; MIN Hongguang

    2011-01-01

    A long time immersion experiment of mortar specimens is carried out to investigate their degradation mechanism by sulfuric acid. Water-cement ratios of mortar are ranging from 0.5 to 0.7 and the pH value of sulfuric acid is 3.5 and 4.0 respectively. The pH meter is used to monitor the soak solution and the titration sulfuric acid with given concentration is added to maintain original pH value, through which the acid consumption of mortar is recorded. A theoretical reaction rate model is also proposed based on concentration boundary layer model. The results show that theoretical model fits the experimental results well and the corrosion mechanism can be modeled by a diffusion process accompanied with an irreversible chemical reaction when pH value of soak solution is no less than 3.5.

  12. Calcitonin substitution in calcitonin deficiency reduces particle-induced osteolysis

    Grabellus Florian

    2011-08-01

    Full Text Available Abstract Background Periprosthetic osteolysis is a major cause of aseptic loosening in joint arthroplasty. This study investigates the impact of CT (calcitonin deficiency and CT substitution under in-vivo circumstances on particle-induced osteolysis in Calca -/- mice. Methods We used the murine calvarial osteolysis model based on ultra-high molecular weight polyethylene (UHMWPE particles in 10 C57BL/6J wild-type (WT mice and twenty Calca -/- mice. The mice were divided into six groups: WT without UHMWPE particles (Group 1, WT with UHMWPE particles (Group 2, Calca -/- mice without UHMWPE particles (Group 3, Calca -/- mice with UHMWPE particles (Group 4, Calca -/- mice without UHMWPE particles and calcitonin substitution (Group 5, and Calca -/- mice with UHMWPE particle implantation and calcitonin substitution (Group 6. Analytes were extracted from serum and urine. Bone resorption was measured by bone histomorphometry. The number of osteoclasts was determined by counting the tartrate-resistant acid phosphatase (TRACP + cells. Results Bone resorption was significantly increased in Calca -/- mice compared with their corresponding WT. The eroded surface in Calca -/- mice with particle implantation was reduced by 20.6% after CT substitution. Osteoclast numbers were significantly increased in Calca -/- mice after particle implantation. Serum OPG (osteoprotegerin increased significantly after CT substitution. Conclusions As anticipated, Calca -/- mice show extensive osteolysis compared with wild-type mice, and CT substitution reduces particle-induced osteolysis.

  13. Mathematical models for foam-diverted acidizing and their applications

    Li Songyan; Li Zhaomin; Lin Riyi

    2008-01-01

    Foam diversion can effectively solve the problem of uneven distribution of acid in layers of different permeabilities during matrix acidizing.Based on gas trapping theory and the mass conservation equation,mathematical models were developed for foam-diverted acidizing,which can be achieved by a foam slug followed by acid injection or by continuous injection of foamed acid.The design method for foam-diverted acidizing was also given.The mathematical models were solved by a computer program.Computed results show that the total formation skin factor,wellhead pressure and bottomhole pressure increase with foam injection,but decrease with acid injection.Volume flow rate in a highpermeability layer decreases,while that in a low-permeability layer increases,thus diverting acid to the low-permeability layer from the high-permeability layer.Under the same formation conditions,for foamed acid treatment the operation was longer,and wellhead and bottomhole pressures are higher.Field application shows that foam slug can effectively block high permeability layers,and improve intake profile noticeably.

  14. Complexation and molecular modeling studies of europium(III)-gallic acid-amino acid complexes.

    Taha, Mohamed; Khan, Imran; Coutinho, João A P

    2016-04-01

    With many metal-based drugs extensively used today in the treatment of cancer, attention has focused on the development of new coordination compounds with antitumor activity with europium(III) complexes recently introduced as novel anticancer drugs. The aim of this work is to design new Eu(III) complexes with gallic acid, an antioxida'nt phenolic compound. Gallic acid was chosen because it shows anticancer activity without harming health cells. As antioxidant, it helps to protect human cells against oxidative damage that implicated in DNA damage, cancer, and accelerated cell aging. In this work, the formation of binary and ternary complexes of Eu(III) with gallic acid, primary ligand, and amino acids alanine, leucine, isoleucine, and tryptophan was studied by glass electrode potentiometry in aqueous solution containing 0.1M NaNO3 at (298.2 ± 0.1) K. Their overall stability constants were evaluated and the concentration distributions of the complex species in solution were calculated. The protonation constants of gallic acid and amino acids were also determined at our experimental conditions and compared with those predicted by using conductor-like screening model for realistic solvation (COSMO-RS) model. The geometries of Eu(III)-gallic acid complexes were characterized by the density functional theory (DFT). The spectroscopic UV-visible and photoluminescence measurements are carried out to confirm the formation of Eu(III)-gallic acid complexes in aqueous solutions.

  15. Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.

    Huang, Ming; Giese, Timothy J; York, Darrin M

    2015-07-01

    Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic

  16. Modeling the influence of organic acids on soil weathering

    Lawrence, Corey; Harden, Jennifer; Maher, Kate

    2014-08-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  17. Modeling the influence of organic acids on soil weathering

    Lawrence, Corey R.; Harden, Jennifer W.; Maher, Kate

    2014-01-01

    Biological inputs and organic matter cycling have long been regarded as important factors in the physical and chemical development of soils. In particular, the extent to which low molecular weight organic acids, such as oxalate, influence geochemical reactions has been widely studied. Although the effects of organic acids are diverse, there is strong evidence that organic acids accelerate the dissolution of some minerals. However, the influence of organic acids at the field-scale and over the timescales of soil development has not been evaluated in detail. In this study, a reactive-transport model of soil chemical weathering and pedogenic development was used to quantify the extent to which organic acid cycling controls mineral dissolution rates and long-term patterns of chemical weathering. Specifically, oxalic acid was added to simulations of soil development to investigate a well-studied chronosequence of soils near Santa Cruz, CA. The model formulation includes organic acid input, transport, decomposition, organic-metal aqueous complexation and mineral surface complexation in various combinations. Results suggest that although organic acid reactions accelerate mineral dissolution rates near the soil surface, the net response is an overall decrease in chemical weathering. Model results demonstrate the importance of organic acid input concentrations, fluid flow, decomposition and secondary mineral precipitation rates on the evolution of mineral weathering fronts. In particular, model soil profile evolution is sensitive to kaolinite precipitation and oxalate decomposition rates. The soil profile-scale modeling presented here provides insights into the influence of organic carbon cycling on soil weathering and pedogenesis and supports the need for further field-scale measurements of the flux and speciation of reactive organic compounds.

  18. Direct influence of C-terminally substituted amino acids in the Dmt-Tic pharmacophore on delta-opioid receptor selectivity and antagonism.

    Balboni, Gianfranco; Salvadori, Severo; Guerrini, Remo; Negri, Lucia; Giannini, Elisa; Bryant, Sharon D; Jinsmaa, Yunden; Lazarus, Lawrence H

    2004-07-29

    A series of 17 analogues were developed on the basis of the general formula H-Dmt-Tic-NH-CH(R)-R' (denotes chirality; R = charged, neutral, or aromatic functional group; R' = -OH or -NH(2)). These compounds were designed to test the following hypothesis: the physicochemical properties of third-residue substitutions C-terminal to Tic in the Dmt-Tic pharmacophore modify delta-opioid receptor selectivity and delta-opioid receptor antagonism through enhanced interactions with the mu-opioid receptor. The data substantiate the following conclusions: (i) all compounds had high receptor affinity [K(i)(delta) = 0.034-1.1 nM], while that for the mu-opioid receptor fluctuated by orders of magnitude [K(i)(mu) = 15.1-3966 nM]; (ii) delta-opioid receptor selectivity [K(i)(mu)/K(i)(delta)] declined 1000-fold from 22,600 to 21; (iii) a C-terminal carboxyl group enhanced selectivity but only as a consequence of the specific residue; (iv) amidated, positive charged residues [Lys-NH(2) (6), Arg-NH(2) (7)], and a negatively charged aromatic residue [Trp-OH (11)] enhanced mu-opioid affinity [K(i)(mu) = 17.0, 15.1, and 15.7 nM, respectively], while Gly-NH(2) (8), Ser-NH(2) (10), and His-OH (12) were nearly one-tenth as active; and (v) D-isomers exhibited mixed effects on mu-opioid receptor affinity (2' 1 microM) except H-Dmt-Tic-Glu-NH(2) (3), which was a partial delta-opioid receptor agonist (IC(50) = 2.5 nM). Thus, these C-terminally extended analogues indicated that an amino acid residue containing a single charge, amino or guanidino functionality, or aromatic group substantially altered the delta-opioid receptor activity profile (selectivity and antagonism) of the Dmt-Tic pharmacophore, which suggests that the C-terminal constituent plays a major role in determining opioid receptor activity as an "address domain".

  19. Super acid catalysed sequential hydrolysis/cycloisomerization of -(acetylenic)benzamides under microwave condition: Synthesis, antinociceptive and antiinflammatory activity of substituted isocoumarins

    Chandrasekaran Praveen; P Dheenkumar; P T Perumal

    2013-01-01

    Synthesis of isocoumarins and related compounds via triflic acid promoted hydrolysis/cyclization sequence of 2-(alkynyl)benzamides under microwave condition was achieved. The substrate scope of the reaction was broad to include not only aromatic but also polyaromatic and heteroaromatic motifs, thus highlighting the significance of this methodology. One-pot operation, short reaction time, good chemical yields and excellent regioselectivity are the advantages of this protocol. All the synthesized compounds were evaluated for their antinociceptive and antiinflammatory activities using in vivo rodent models.

  20. PERFORMANCE OF PULVERIZED SLAG-SUBSTITUTED CEMENT

    1999-01-01

    The Portland cement is equivalently substituted by slag micropowders with various specific areas. The workability,activity and acid-corrosion resistance of the slag-substituted cements are investigated,the activation of gypsum is discussed,also the porosity and pore distribution of mortars of the slag micropowders cement are determined by mercury intrusion porosimetry.

  1. Modelling the influence of inulin as a fat substitute in comminuted meat products on their physico-chemical characteristics and eating quality using a mixture design approach.

    Keenan, Derek F; Resconi, Virginia C; Kerry, Joseph P; Hamill, Ruth M

    2014-03-01

    The effects of fat substitution using two commercial inulin products on the physico-chemical properties and eating quality of a comminuted meat product (breakfast sausage) were modelled using a specialised response surface experiment specially developed for mixtures. 17 treatments were assigned representing a different substitution level for fat with inulin. Sausages were formulated to contain pork shoulder, back fat/inulin, water, rusk and seasoning (44.3, 18.7, 27.5, 7 and 2.5% w/w). Composition, sensory, instrumental texture and colour characteristics were assessed. Fructan analysis showed that inulin was unaffected by heat or processing treatments. Models showed increasing inulin inclusions decreased cook loss (pinulin concentration, with panellists also scoring products containing inulin as less tender (pinulin to deliver a prebiotic health effect.

  2. Selective substitution of amino acids limits proteolytic cleavage and improves the bioactivity of an anti-biofilm peptide that targets the periodontal pathogen, Porphyromonas gingivalis.

    Daep, Carlo Amorin; Novak, Elizabeth A; Lamont, Richard J; Demuth, Donald R

    2010-12-01

    The interaction of the periodontal pathogen, Porphyromonas gingivalis, with oral streptococci such as Streptococcus gordonii precedes colonization of the subgingival pocket and represents a target for limiting P. gingivalis colonization of the oral cavity. Previous studies showed that a synthetic peptide (designated BAR) derived from the antigen I/II protein of S. gordonii was a potent competitive inhibitor of P. gingivalis adherence to S. gordonii and subsequent biofilm formation. Here we show that despite its inhibitory activity, BAR is rapidly degraded by intact P. gingivalis cells in vitro. However, in the presence of soluble Mfa protein, the P. gingivalis receptor for BAR, the peptide is protected from proteolytic degradation suggesting that the affinity of BAR for Mfa is higher than for P. gingivalis proteases. The rate of BAR degradation was reduced when the P. gingivalis lysine-specific gingipain was inhibited using the specific protease inhibitor, z-FKcK, or when the gene encoding the Lys-gingipain was inactivated. In addition, substituting d-Lys for l-Lys residues in BAR prevented degradation of the peptide when incubated with the Lys-gingipain and increased its specific adherence inhibitory activity in a S. gordonii-P. gingivalis dual species biofilm model. These results suggest that Lys-gingipain accounts in large part for P. gingivalis-mediated degradation of BAR and that more effective peptide inhibitors of P. gingivalis adherence to streptococci can be produced by introducing modifications that limit the susceptibility of BAR to the Lys-gingipain and other P. gingivalis associated proteases.

  3. Nitric acid: modeling osmotic coefficients and acid-base dissociation using the BIMSA theory.

    Ruas, Alexandre; Pochon, Patrick; Simonin, Jean-Pierre; Moisy, Philippe

    2010-11-14

    This work is aimed at a description of the thermodynamic properties of highly concentrated aqueous solutions of nitric acid salts at 25 °C within the binding mean spherical approximation (BIMSA) theory. The predictive capability of this model was examined. First, Raman spectroscopy was used to study the proportion of associated nitric acid as a function of concentration. The corresponding apparent association constant values were compared with literature values. Besides, the BIMSA model, taking into account complex formation, was used to represent literature experimental osmotic coefficient variation with concentration. This theoretical description led to an assessment of the degree of association. The so calculated amount of associated nitric acid coincides accurately with our Raman experimental results up to a high concentration of acid.

  4. Nitric acid: modeling osmotic coefficients and acid-base dissociation using the BIMSA theory

    Ruas, A.; Pochon, P.; Moisy, Ph. [CEA Marcoule, Nucl Energy Div, RadioChem and Proc Dept, F-30207 Bagnols Sur Ceze (France); Simonin, J. P. [Univ Paris 06, CNRS, UMR 7195, Lab PECSA, F-75252 Paris 05, (France)

    2010-07-01

    This work is aimed at a description of the thermodynamic properties of highly concentrated aqueous solutions of nitric acid salts at 25 C within the binding mean spherical approximation (BIMSA) theory. The predictive capability of this model was examined. First, Raman spectroscopy was used to study the proportion of associated nitric acid as a function of concentration. The corresponding apparent association constant values were compared with literature values. Besides, the BIMSA model, taking into account complex formation, was used to represent literature experimental osmotic coefficient variation with concentration. This theoretical description led to an assessment of the degree of association. The so calculated amount of associated nitric acid coincides accurately with our Raman experimental results up to a high concentration of acid. (authors)

  5. 羟基肉桂酸锗氮桥环化合物在乌鸡饲料中的应用%The Application of Germatranes of Hydroxyl Substituted Cinnamic Acid Compounds in the Diet of Gallus domesticus Brisson

    田伟; 陈晓东

    2012-01-01

    [Objective] By using germatranes of hydroxyl substituted cinnamic acid compounds as additives, the effects of adding it in the diet of Gallus domesticus Brisson on biochemical indexes were studied. [ Method] Adding germatranes of p - ,o - ,m - hydroxyl substituted cinnamic acid to the diet with 40 mg/kg for each,their weight,melanin content, fat content were measured when chickens are at 30,60,75,90,120 day old age. [ Result ] Adding cinnamic acid germanium in the diet of Gallus domesticus Brisson could improve weight, increase melanin content, decrease fat content,while germatranes of p - ,o - ,m - hydroxyl substituted cinnamic acid have no significant differences. [ Conclusion] .The study will provide theoretical basis for the application of germanium addictives in Gallus domesticus Brisson production.%[目的]以羟基肉桂酸锗氮桥环化合物为添加剂,研究将其添加于乌鸡日粮中对乌鸡生化指标的影响.[方法]以邻、对、间羟基肉桂酸锗各40 mg/kg添加到日粮中,分别在30、60、75、90、120日龄时,测定乌鸡的体重、黑色素含量、脂肪含量.[结果]在乌鸡饲料中添加肉桂酸锗均能提高乌鸡体重,增加黑色素含量,降低脂肪含量,而邻、对、间羟基肉桂酸锗之间无显著差异.[结论]该研究为锗添加剂在乌骨鸡生产中的应用提供了理论依据.

  6. Single amino-acid substitution in the N-terminal arm altered the tetramer stability of rat muscle lactate dehydrogenase A

    YUAN; Chong; (

    2001-01-01

    [1]Price, N. C., Assembly of multi-subunit structures, in Mechanisms of Protein Folding (ed. Pain, R. H.), New York: Oxford University Press, 1994, 160-193.[2]Casal, J. I., Ahern, T. J., Davenport, R. C. et al., Subunit interface of triosephosphate isomerase: Site-directed mutagenesis and characterization of the altered enzyme, Biochemistry, 1987, 26: 1258-1264.[3]Chakerian, A. E., Matthews, K. S., Characterization of mutations in oligomerization domain of lac repressor protein, J. Biol. Chem., 1991, 266: 22206-22214.[4]Mandelman, D., Schwarz, F. P., Li, H. Y. et al., The role of quaternary interactions on the stability and activity of ascorbate peroxidase, Protein Sci., 1998, 7: 2089-2098.[5]Thomas, M. C., Ballantine, S. P., Bethell, S. S. et al., Single amino acid substitutions disrupt tetramer formation in the dihydroneopterin aldolase enzyme of Pneumocystis carinii, Biochemistry, 1998, 37: 11629-11636.[6]Holbrook, J. J., Liljas, A., Steindel, S. J. et al., Lactate dehydrogenase, in The Enzymes (ed. Boyer, P. D.), Vol. 11, 3rd ed., New York: Academic Press, 1975, 191-292.[7]Zettlmeissl, G., Rudolph, R., Jaenicke, R., Reconstitution of lactic dehydrogenase after acid dissociation, Eur. J. Biochem., 1981, 121: 169-175.[8]Zettlmeissl, G., Rudolph, R., Jaenicke, R., Rate-determining folding and association reactions on the reconstitution pathway of porcine skeletal muscle lactic dehydrogenase after denaturation by guanidine hydrochloride, Biochemistry, 1982, 21: 3946-3950.[9]Hermann, R., Jaenicke, R., Rudolph, R., Analysis of the reconstitution of oligomeric enzymes by cross-linking with glutaraldehyde: Kinetics of reassociation of lactic dehydrogenase, Biochemistry, 1981, 20: 5195-5201.[10]Jaenicke, R., Folding and association of protein, Prog. Biophys. Mol. Biol., 1987, 49: 117-237.[11]Opitz, U., Rudolph, R., Jaenicke, R. et al., Proteolytic dimeric of porcine muscle lactate dehydrogenase: Characterization, folding, and

  7. Modelling dimercaptosuccinic acid (DMSA) plasma kinetics in humans

    van Eijkeren, Jan C H; Olie, J Daniël N; Bradberry, Sally M; Vale, J Allister; de Vries, Irma; Meulenbelt, Jan; Hunault, Claudine C

    2016-01-01

    CONTEXT: No kinetic models presently exist which simulate the effect of chelation therapy on lead blood concentrations in lead poisoning. OBJECTIVE: Our aim was to develop a kinetic model that describes the kinetics of dimercaptosuccinic acid (DMSA; succimer), a commonly used chelating agent, that c

  8. Acid hydrolysis of corn stover using hydrochloric acid: Kinetic modeling and statistical optimization

    Sun Yong

    2014-01-01

    Full Text Available The hydrolysis of corn stover using hydrochloric acid was studied. The kinetic parameters of the mathematical models for predicting the yields of xylose, glucose, furfural and acetic acid were obtained, and the corresponding xylose generation activation energy of 100 kJ/mol was determined. The characterization of corn stover using with different techniques during hydrolysis indicated an effective removal of xylan and the slightly alteration on the structures of cellulose and lignin. A 23five levels Central Composite Design (CCD was used to develop a statistical model for the optimization of process variables including acid concentration, pretreatment temperature and time. The optimum conditions determined by this model were found to be 108ºC for 80 minutes with acid concentration of 5.8%. Under these conditions, the maximised results are the following: xylose 19.93 g/L, glucose 1.2 g/L, furfural 1.5 g/L, acetic acid 1.3 g/L. The validation of the model indicates a good agreement between the experimental results and the predicted values.

  9. Amino acid substitutions in the melanoma antigen recognized by T cell 1 peptide modulate cytokine responses in melanoma-specific T cells

    Nielsen, M B; Kirkin, A F; Loftus, D

    2000-01-01

    enhances the production of mRNA for interleukin (IL)-5, IL-10, IL-13, IL-15, and interferon-gamma and significantly enhances release of IL-13 and IL-10 from anti-MART-1 cytotoxic T cells. Another heteroclitic peptide, 1L, with an A to L substitution in MART-1(27-35), also enhances the tyrosine...

  10. Predicting nucleic acid binding interfaces from structural models of proteins.

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure.

  11. Synthesis and antiinflammatory activity of substituted (2-oxochromen-3-ylbenzamides

    Maddi V

    2007-01-01

    Full Text Available The title compounds were synthesized by condensing 3-aminocoumarin with substituted aromatic acid chlorides. The acid chlorides were prepared from different substituted aromatic carboxylic acids and thionyl chloride. The structures of the compounds were confirmed by IR, NMR spectral data and elemental analysis. The title compounds were found to possess significant anti-inflammatory and analgesic activities.

  12. Factor substitution in nursing homes.

    Cawley, John; Grabowski, David C; Hirth, Richard A

    2006-03-01

    This paper studies factor substitution in one important sector: the nursing home industry. Specifically, we measure the extent to which nursing homes substitute materials for labor when labor becomes relatively more expensive. From a policy perspective, factor substitution in this market is important because materials-intensive methods of care are associated with greater risks of morbidity and mortality among nursing home residents. Studying longitudinal data from 1991 to 2000 on nearly every nursing home in the United States, we use the method of instrumental variables (IV) to address measurement error in nursing home wages. The results from the IV models yield evidence of factor substitution: higher nursing home wages are associated with greater use of psychoactive drugs and lower quality.

  13. Pharmacological characterization of LY233053: A structurally novel tetrazole-substituted competitive N-methyl-D-aspartic acid antagonist with a short duration of action

    Schoepp, D.D.; Ornstein, P.L.; Leander, J.D.; Lodge, D.; Salhoff, C.R.; Zeman, S.; Zimmerman, D.M. (Eli Lilly and Company, Indianapolis, IN (USA))

    1990-12-01

    This study reports the activity of a structurally novel excitatory amino acid receptor antagonist, LY233053 (cis-(+-)-4-((2H-tetrazol-5-yl)methyl)piperidine-2-carboxylic acid), the first tetrazole-containing competitive N-methyl-D-aspartic acid (NMDA) antagonist. LY233053 potently inhibited NMDA receptor binding to rat brain membranes as shown by the in vitro displacement of (3H) CGS19755 (IC50 = 107 +/- 7 nM). No appreciable affinity in (3H)alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) or (3H)kainate binding assays was observed (IC50 values greater than 10,000 nM). In vitro NMDA receptor antagonist activity was further demonstrated by selective inhibition of NMDA-induced depolarization in cortical wedges (IC50 = 4.2 +/- 0.4 microM vs. 40 microM NMDA). LY233053 was effective after in vivo systemic administration in a number of animal models. In neonatal rats, LY233053 selectively blocked NMDA-induced convulsions (ED50 = 14.5 mg/kg i.p.) with a relatively short duration of action (2-4 hr). In pigeons, LY233053 potently antagonized (ED50 = 1.3 mg/kg i.m.) the behavioral suppressant effects of 10 mg/kg of NMDA. However, a dose of 160 mg/kg, i.m., was required to produce phencyclidine-like catalepsy in pigeons. In mice, LY233053 protected against maximal electroshock-induced seizures at lower doses (ED50 = 19.9 mg/kg i.p.) than those that impaired horizontal screen performance (ED50 = 40.9 mg/kg i.p.). Cholinergic and GABAergic neuronal degenerations after striatal infusion of NMDA were prevented by single or multiple i.p. doses of LY233053. In summary, the antagonist activity of LY233053 after systemic administration demonstrates potential therapeutic value in conditions of neuronal cell loss due to NMDA receptor excitotoxicity.

  14. Design, Synthesis and Anti-HIV Integrase Evaluation of 1,2,3-Triazol-4-yl-substituted 1,4-Dihydro-4-oxo-1,5-napthyridine-3-carboxylic Acids

    ZENG,Jia; L(U),Xiuhua; ZENG,Chengchu; HU,Liming; ZHONG,Rugang

    2009-01-01

    Copper(I)-eatalyzed terminal alkyne-azide 1,3-cycloaddition reaction has emerged as one of the main strategies for the rapid creation and screening of a small molecular library. The present work describes the design and synthe-sis of a series of 1,2,3-triazol-4-yl-substituted 1,4-dihydro-4-oxo-1,5-napthyridine-3-carboxylic acids in which the hydrophobic and hydrophilic domains were efficiently incorporated by a click reaction. The structures of the desired products 8 and 12 were characterized by spectroscopic methods and their HIV integrase inhibitory activities were also screened.

  15. The evolutionary appearance of non-cyanogenic hydroxynitrile glucosides in the Lotus genus is accompanied by the substrate specialization of paralogous beta-glucosidases resulting from a crucial amino acid substitution

    Lai, Daniela; Abou Hachem, Maher; Robson, Fran;

    2014-01-01

    with the Lotus corniculatus clade within the Lotus genus. This suggests the evolutionary scenario that substrate specialization for rhodiocyanosides evolved from a promiscuous activity of a progenitor cyanogenic beta-glucosidase, resembling BGD2, and required no more than a single amino acid substitution.......Lotus japonicus, like several other legumes, biosynthesizes the cyanogenic alpha-hydroxynitrile glucosides lot-australin and linamarin. Upon tissue disruption these compounds are hydrolysed by a specific beta-glucosidase, resulting in the release of hydrogen cyanide. Lotus japonicus also produces...

  16. Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

    Paul, Bijan Kumar [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India); Guchhait, Nikhil, E-mail: nikhil.guchhait@rediffmail.com [Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009 (India)

    2013-02-01

    Highlights: ► Intramolecular hydrogen bonding (IMHB) in salicylic acid and its chloro derivatives. ► A complex effect of +R and −I effect of chlorine substituents on IMHB energy. ► Interplay between IMHB energy and aromaticity. ► Directional nature of IMHB from quantum chemical assessment. ► Quantum chemical treatment vs. geometrical criteria to assess weak interaction. - Abstract: Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇{sup 2}ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems.

  17. Investigation of properties of copper, ferrous complexes with 1-(5-bromo-2-pyridylazo)-2-naphthol-6-sulphonic acid and application of substitution reaction in metallic complex to selective determination of trace amounts of metal.

    Gao, H W

    2000-08-16

    The report was the first to establish the new method for the selective determination of trace amounts of metal using the substitution reaction in metallic complex. The reactions between copper(II) and 1-(5-bromo-2-pyridylazo)-2-naphthol-6-sulphonic acid (BPANS) and between ferrous(II) and BPANS at pH 3.5 were studied. In absence of any masking reagent, the recommended method was selective in the determination of trace amounts of copper with Fe-BPANS complex as chromogenic reagent because copper(II) can substitute Fe from Fe-BPANS complex to form Cu-BPANS complex. The ordinary spectrophotometric method was unsuitable to the substitution reaction because the excess of Fe-BPANS complex had the high absorption and affected seriously the absorption of Cu-BPTANS complex. The spectral correction principle may eliminate the above influence to give the simple determination of the composition ratio, stepwise absorptivity (epsilon) and stability constant (K) of metal complex. For analysis of samples, the recovery of copper was between 96.5 and 106% with R.S.D. less than 5%.

  18. A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model.

    Maurer, Patrick; Thomas, Vibin; Rivard, Ugo; Iftimie, Radu

    2010-07-28

    Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Bronsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa congruent with 1) as a model for excited-state HPTS( *) (pKa congruent with 1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

  19. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis

    Durruty, Ignacio; Aguirrezábal, Luis A. N.; Echarte, María M.

    2016-01-01

    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ′) while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809

  20. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit.

  1. A Bilayer Engineered Skin Substitute for Wound Repair in an Irradiation-Impeded Healing Model on Rat

    2015-01-01

    Objective: An engineered skin substitute is produced to accelerate wound healing by increasing the mechanical strength of the skin wound via high production of collagen bundles. During the remodeling stage of wound healing, collagen deposition is the most important event. The collagen deposition process may be altered by nutritional deficiency, diabetes mellitus, microbial infection, or radiation exposure, leading to impaired healing. This study describes the fabrication of an engineered bila...

  2. Novel Caffeic Acid Nanocarrier: Production, Characterization, and Release Modeling

    Milad Fathi

    2013-01-01

    Full Text Available This paper deals with the development of novel nanocarriers using layer by layer carbohydrate coating of caffeic acid loaded solid lipid nanoparticles (SLNs to improve stability and colon delivery of the poorly water-soluble caffeic acid. Three biopolymers (chitosan, alginate, and pectin in different concentrations (0.1, 0.25, and 0.5% were electrostatically coated over the SLN surface. The size and zeta potential of produced nanocarriers were measured using photon correlation spectroscopy. Mathematical models (i.e., zero-order, first-order, Higuchi, Ritger-Peppas, reciprocal powered time, Weibull, and quadratic models were used to describe the release and kinetic modeling in gastrointestinal solution (GIS. Also, antioxidant activity of caffeic acid during the release in GIS was investigated using DPPH and reducing activity methods. The prepared treatments coated by alginate-chitosan as well as pectin-chitosan coated SLN at the concentration of 0.1% showed nanosized bead; the latter efficiently retarded the release of caffeic acid in gastric media up to 2.5 times higher than that of SLN. Zeta potential values of coated samples were found to significantly increase in comparison to SLN indicating the higher stability of produced nanocarriers. Antioxidant activity of caffeic acid after gastric release did not result in the same trend as observed for caffeic acid release from different treatments; however, in line with less caffeic acid release in the intestine solution by the effect of coating, lower antioxidant activity was determined at the end stage of the experiment.

  3. Histological and histomorphometrical analysis of a silica matrix embedded nanocrystalline hydroxyapatite bone substitute using the subcutaneous implantation model in Wistar rats

    Ghanaati, Shahram; Orth, Carina; Barbeck, Mike; Kirkpatrick, Charles James [Institute of Pathology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstrasse 1, 55101 Mainz (Germany); Willershausen, Ines [Institute for Dental Material Sciences and Technology, University Medical Center of the Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 14, 55128 Mainz (Germany); Thimm, Benjamin W [Institute for Biomechanics, ETH Zuerich, Wolfgang-Pauli-Str.10, 8093 Zuerich (Switzerland); Booms, Patrick [Leeds Institute of Molecular Medicine, Section of Medicine, Surgery and Anaesthesia, University of Leeds (United Kingdom); Stuebinger, Stefan; Landes, Constantin; Sader, Robert Anton, E-mail: ghanaati@uni-mainz.d [Department for Oral, Cranio-Maxillofacial and Facial Plastic Surgery, Medical Center of the Goethe University Frankfurt, Theodor-Stein-Kai 7, 60596 Frankfurt am Main (Germany)

    2010-06-01

    The clinical suitability of a bone substitute material is determined by the ability to induce a tissue reaction specific to its composition. The aim of this in vivo study was to analyze the tissue reaction to a silica matrix-embedded, nanocrystalline hydroxyapatite bone substitute. The subcutaneous implantation model in Wistar rats was chosen to assess the effect of silica degradation on the vascularization of the biomaterial and its biodegradation within a time period of 6 months. Already at day 10 after implantation, histomorphometrical analysis showed that the vascularization of the implantation bed reached its peak value compared to all other time points. Both vessel density and vascularization significantly decreased until day 90 after implantation. In this time period, the bone substitute underwent a significant degradation initiated by TRAP-positive and TRAP-negative multinucleated giant cells together with macrophages and lymphocytes. Although no specific tissue reaction could be related to the described silica degradation, the biomaterial was close to being fully degraded without a severe inflammatory response. These characteristics are advantageous for bone regeneration and remodeling processes.

  4. Ab initio and kinetic modeling studies of formic acid oxidation

    Marshall, Paul; Glarborg, Peter

    2015-01-01

    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based...... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...

  5. Enhanced Stability of the Model Mini-protein in Amino Acid Ionic Liquids and Their Aqueous Solutions

    Chevrot, Guillaume; Chaban, Vitaly V

    2015-01-01

    Using molecular dynamics simulations, the structure of model mini-protein was thoroughly characterized in the imidazolium-based amino acid ionic liquids and their aqueous solutions. We report that the mini-protein is more stable when AAIL is added as a cosolvent. Complete substitution of water by organic cations and anions further results in hindered conformational flexibility of the mini-protein. This observation suggests that AAILs are able to defend proteins from thermally induced denaturation. We show by means of radial distributions that the mini-protein is efficiently solvated by both solvents due to agood mutual miscibility. However, amino acid based anions prevail in the first coordination sphere of the mini-protein.

  6. Preparation of Peracetic Acid from Acetic Acid and Hydrogen Peroxide: Experimentation and Modeling

    赵雪冰; 张婷; 周玉杰; 刘德华

    2008-01-01

    Based on the kinetic equations and equilibrium constants, some mathematic models were developed for calculating peracetic acid (PAA) concentration, equilibrium conversion rate of hydrogen peroxide, etc. The effects of several parameters on PAA synthesis were investigated by experimentation and modeling. The equilibrium constants determined from the forward and reverse rate constants at 293, 303,313 and 323 K were 2.91, 2.81, 2.72 and 2.63, respectively. The models could predict the values of equilibrium concentration of PAA with average relative deviation of less than 10%. Both of the experimental and model-calculated results demonstrated that temperature and catalyst loading were the most important factors affecting the rate of PAA synthesis, but high temperature led to the decrease of equilibrium concentration of PAA. According to the model, the reaction could achieve equilibrium within 24 h when operated at 303 K with 1%~1.5%(ω) sulfuric acid as catalyst. Additionally, when using anhydrous acetic acid and 30% hydrogen peroxide to prepare PAA, the volumetric ratio of the two solutions should be in the range of 1.2~1.5 in order to obtain the highest equilibrium concentration of PAA. This study can serve as a step towards the further optimization of PAA synthesis and some other related investigations.

  7. Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

    Paul, Bijan Kumar; Guchhait, Nikhil

    2013-02-01

    Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems.

  8. Water-stable helical structure of tertiary amides of bicyclic β-amino acid bearing 7-azabicyclo[2.2.1]heptane. Full control of amide cis-trans equilibrium by bridgehead substitution.

    Hosoya, Masahiro; Otani, Yuko; Kawahata, Masatoshi; Yamaguchi, Kentaro; Ohwada, Tomohiko

    2010-10-27

    Helical structures of oligomers of non-natural β-amino acids are significantly stabilized by intramolecular hydrogen bonding between main-chain amide moieties in many cases, but the structures are generally susceptible to the environment; that is, helices may unfold in protic solvents such as water. For the generation of non-hydrogen-bonded ordered structures of amides (tertiary amides in most cases), control of cis-trans isomerization is crucial, even though there is only a small sterical difference with respect to cis and trans orientations. We have established methods for synthesis of conformationally constrained β-proline mimics, that is, bridgehead-substituted 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acids. Our crystallographic, 1D- and 2D-NMR, and CD spectroscopic studies in solution revealed that a bridgehead methoxymethyl substituent completely biased the cis-trans equilibrium to the cis-amide structure along the main chain, and helical structures based on the cis-amide linkage were generated independently of the number of residues, from the minimalist dimer through the tetramer, hexamer, and up to the octamer, and irrespective of the solvent (e.g., water, alcohol, halogenated solvents, and cyclohexane). Generality of the control of the amide equilibrium by bridgehead substitution was also examined.

  9. A model for the linear stability of the interface between aqueous humor and vitreous substitutes after vitreoretinal surgery

    Isakova, Krystyna; Pralits, Jan O.; Repetto, Rodolfo; Romano, Mario R.

    2014-12-01

    We consider the motion of two immiscible viscous fluids induced by periodic oscillations of a flat solid surface along its plane. The interface between the two fluids is parallel to the solid wall; one fluid occupies the region between the wall and the interface and the other extends from the interface to infinity. We study numerically the linear stability of the interface with respect to two-dimensional perturbations using the normal mode analysis and assuming quasi-steady flow conditions. The analysis is motivated by the need of understanding the behavior of vitreous substitutes inserted in the vitreous chamber of the eye after vitrectomy. This is a common surgical procedure adopted to treat retinal detachments, whereby the vitreous humor is removed from the eye and replaced by fluids immiscible with water. Owing to their hydrophobic nature, vitreous substitutes coexist in the vitreous chamber with a certain amount of aqueous humor (the fluid produced in the anterior part of the eye) and, typically, a thin layer of aqueous separates the tamponade fluid from the retina. A common problem with this treatment is that, in some cases, the interface between the two fluids breaks down and this might eventually lead to the generation of an emulsion. It is believed that mechanics plays an important role in this process but the problem remains very poorly understood. We find that instability of the interface is possible in a range of parameters that is relevant for the problem that motivated the present analysis. This suggests that shear instability is likely a possible mechanism triggering the onset of vitreous substitutes-aqueous interface instability.

  10. Computational model of abiogenic amino acid condensation to obtain a polar amino acid profile.

    Polanco, Carlos; Buhse, Thomas; Samaniego, José Lino; Castañón González, Jorge Alberto; Arias Estrada, Miguel

    2014-01-01

    In accordance with the second law of thermodynamics, the Universe as a whole tends to higher entropy. However, the sequence of far-from-equilibrium events that led to the emergence of life on Earth could have imposed order and complexity during the course of chemical reactions in the so-called primordial soup of life. Hence, we may expect to find characteristic profiles or biases in the prebiotic product mixtures, as for instance among the first amino acids. Seeking to shed light on this hypothesis, we have designed a high performance computer program that simulates the spontaneous formation of the amino acid monomers in closed environments. The program was designed in reference to a prebiotic scenario proposed by Sydney W. Fox. The amino acid abundances and their polarities as the two principal biases were also taken into consideration. We regarded the computational model as exhaustive since 200,000 amino acid dimers were formed by simulation, subsequently expressed in a vector and compared with the corresponding amino acid dimers that were experimentally obtained by Fox. We found a very high similarity between the experimental results and our simulations.

  11. Diffusion model for acid corrosion of cemented materials

    Van Dijk, J.C.; De Moel, P.J.; Nooyen, W.F.; Nuiten, P.C.

    1986-09-25

    The acid corrosion of cemented materials is an important aspect in engineering practice. Corrosion affects the strength of materials and may cause a deterioration of water quality. This article deals with corrosion due to non-erosive acid attacks. A diffusion model is presented in which the depth of attack increases in proportion to the square root of both time, the hydronium ion concentration in the water, and the inverse of the total concentration of lime in the solid phase. Experiments verifying the model are presented. The experiments also reveal that the corrosion of asbestos cement proceeds faster as compared to concrete because of desintegration of the structure of asbestos cement. The diffusion model also worked out to be applicable for corrosion by agressive CO/sub 2/. The lower corrosion rate due to the formation of CaCO/sub 3/ can for this case be described by a lower diffusion coefficient. 4 tabs., 6 figs., 9 refs.

  12. Alanine or aspartic acid substitutions at serine23/24 of cardiac troponin I decrease thin filament activation, with no effect on crossbridge detachment kinetics

    Mamidi, Ranganath; Gollapudi, Sampath K.; Mallampalli, Sri Lakshmi; Chandra, Murali

    2012-01-01

    Ala/Asp substitutions at Ser23/24 have been employed to investigate the functional impact of cardiac troponin I (cTnI) phosphorylation by protein kinase A (PKA). Some limitations of previous studies include the use of heterologous proteins and confounding effects arising from phosphorylation of cardiac myosin binding protein-C. Our goal was to probe the effects of cTnI phosphorylation using a homologous assay, so that altered function could be solely attributed to changes in cTnI. We reconstituted detergent-skinned rat cardiac papillary fibers with homologous rat cardiac troponin subunits to study the impact of Ala and Asp substitutions at Ser23/24 of rat cTnI (RcTnI S23A/24A and RcTnI S23D/24D). Both RcTnI S23A/24A and RcTnI S23D/24D showed a ~36% decrease in Ca2+-activated maximal tension. Both RcTnI S23A/24A and RcTnI S23D/24D showed a ~18% decrease in ATPase activity. Muscle fiber stiffness measurements suggested that the decrease in thin filament activation observed in RcTnI S23A/24A and RcTnI S23D/24D was due to a decrease in the number of strongly-bound crossbridges. Another major finding was that Ala and Asp substitutions in cTnI did not affect crossbridge detachment kinetics. PMID:22684024

  13. Synthesis of novel 5-alkyl/aryl/heteroaryl substituted diethyl 3,4-dihydro-2H-pyrrole-4,4-dicarboxylates by aziridine ring expansion of 2-[(aziridin-1-yl-1-alkyl/aryl/heteroaryl-methylene]malonic acid diethyl esters

    U. K. Syam Kumar

    2011-06-01

    Full Text Available A novel synthetic methodology has been developed for the synthesis of diethyl 5-alkyl/aryl/heteroaryl substituted 3,4-dihydro-2H-pyrrole-4,4-dicarboxylates (also called 2-substituted pyrroline-4,5-dihydro-3,3-dicarboxylic acid diethyl esters by iodide ion induced ring expansion of 2-[(aziridin-1-yl-1-alkyl/aryl/heteroaryl-methylene]malonic acid diethyl esters in very good to excellent yields under mild reaction conditions. The electronic and steric impact of the substituents on the kinetics of ring expansion of N-vinyl aziridines to pyrrolines has been studied. Various diversely substituted novel pyrroline derivatives have been synthesized by this methodology and the products can be used as key intermediates in the synthesis of substituted pyrrolines, pyrroles and pyrrolidines.

  14. Modeling acid-gas generation from boiling chloride brines

    Sonnenthal Eric

    2009-11-01

    Full Text Available Abstract Background This study investigates the generation of HCl and other acid gases from boiling calcium chloride dominated waters at atmospheric pressure, primarily using numerical modeling. The main focus of this investigation relates to the long-term geologic disposal of nuclear waste at Yucca Mountain, Nevada, where pore waters around waste-emplacement tunnels are expected to undergo boiling and evaporative concentration as a result of the heat released by spent nuclear fuel. Processes that are modeled include boiling of highly concentrated solutions, gas transport, and gas condensation accompanied by the dissociation of acid gases, causing low-pH condensate. Results Simple calculations are first carried out to evaluate condensate pH as a function of HCl gas fugacity and condensed water fraction for a vapor equilibrated with saturated calcium chloride brine at 50-150°C and 1 bar. The distillation of a calcium-chloride-dominated brine is then simulated with a reactive transport model using a brine composition representative of partially evaporated calcium-rich pore waters at Yucca Mountain. Results show a significant increase in boiling temperature from evaporative concentration, as well as low pH in condensates, particularly for dynamic systems where partial condensation takes place, which result in enrichment of HCl in condensates. These results are in qualitative agreement with experimental data from other studies. Conclusion The combination of reactive transport with multicomponent brine chemistry to study evaporation, boiling, and the potential for acid gas generation at the proposed Yucca Mountain repository is seen as an improvement relative to previously applied simpler batch evaporation models. This approach allows the evaluation of thermal, hydrological, and chemical (THC processes in a coupled manner, and modeling of settings much more relevant to actual field conditions than the distillation experiment considered. The actual

  15. Currency substitution, portfolio diversification, and money demand

    Freitas, Miguel Lebre de; Veiga, Francisco José

    2006-01-01

    We extend the Thomas (1985) dynamic optimising model of money demand and currency substitution to the case in which the individual has restricted or no access to foreign currency denominated bonds. In this case Currency Substitution decisions and Asset Substitution decisions are not separable. The results obtained suggest that the significance of an expected exchange rate depreciation term in the demand for domestic money provides a valid test for the presence of currency subst...

  16. Design, synthesis, antitumor evaluations and molecular modeling studies of novel 3,5-substituted indolin-2-one derivatives

    Hai-hong LI; Jian DING; Hua-liang JIANG; Xiu-hua ZHANG; Jin-zhi TAN; Li-li CHEN; Hong LIU; Xiao-min LUO; Xu SHEN; Li-ping LIN; Kai-xian CHEN

    2007-01-01

    Aim: To design and synthesize a novel class of antitumor agents, featuring the 3,5-substituted indolin-2-one framework. Methods: Based on enzyme binding fea-tures of (Z)-SU5402, introducing a β-pyrrole group at the 3-position of the indolin-2-one core, a series of novel 3,5-substituted indolin-2-ones were designed and synthesized. Four human Carcinoma cell lines of A-431, A-549, MDA-MB-468,and Autosomal Dominant Polycystic Kidney disease were chosen for the cell proliferation assay. Results: Twenty new compounds (la-t) with E configuration have been designed, synthesized and bioassayed. Their structural features were determined by nuclear magnetic resonance (NMR) spectra, low- and high-resolu-tion mass spectra, and confirmed by X-ray crystallography. Although the enzyme assay showed a weak inhibition effect against the epidermal growth factor receptor, vascular endothelial growth factor receptor, fibroblast growth factor receptor and platelet-derived growth factor receptor tyrosine kinases, the cell-based antitumor activity was promising. Compounds 1g and 1h showed higher inhibitory activity toward the A-549 and MDA-MB-468 cell lines with IC50 of 0.065-9.4 μmol/L. Conclusion: This study provides a new template for further development of potent antitumor drugs.

  17. The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: molecular modeling and QSAR.

    Jarmuła, Adam; Cieplak, Piotr; Krygowski, Tadeusz M; Rode, Wojciech

    2007-03-15

    Thymidylate synthase (TS) is a target enzyme for a number of anticancer agents including the 5-fluorouracil metabolite, FdUMP. The present paper reports on molecular modeling studies of the effect of substitution at C(5) position in the pyrimidine ring of the TS substrate, dUMP, on the binding affinity for the enzyme. The results of molecular dynamics simulations show that the binding of C(5) analogues of dUMP to TS in the binary complexes does not undergo changes, unless a substituent with a large steric effect, such as the propyl group, is involved. On the other hand, apparent differences in the binding of the TS cofactor, resulting from varying substitution at dUMP C(5), are observed in the modeled structures of the ternary complexes of TS. These binding characteristics are supplemented with a classical QSAR model quantifying the relation between the affinity for TS and the substituent electronic and steric effects of C(5) analogues of dUMP. Based on the findings from the present work, the perspectives for finding promising new C(5) analogues of dUMP as potential agents targeted against TS are discussed.

  18. Pre-clinical evaluation of soybean-based wound dressings and dermal substitute formulations in pig healing and non-healing in vivo models

    Rostislav V Shevchenko

    2014-10-01

    Full Text Available In the last decade, a new class of natural biomaterials derived from de-fatted soybean flour processed by either thermoset or extraction procedures has been developed. These biomaterials uniquely combine adaptability to various clinical applications to proven tissue regeneration properties. In the present work, the biomaterials were formulated either as hydrogel or as paste formulation and their potential as wound dressing material or as dermal substitute was assessed by two in vivo models in pig skin: The healing full-thickness punch biopsy model and the non-healing full-thickness polytetrafluoroethylene (PTFE chamber model. The results clearly show that collagen deposition is induced by the presence of these biomaterials. A unique pattern of early inflammatory response, eliciting neutrophils and controlling macrophage infiltration, is followed by tissue cell colonization of the wound bed with a significant deposition of collagen fibers. The study also highlighted the importance in the use of optimal formulations and appropriate handling upon implantation. In large size, non-healing wounds, wound dermis was best obtained with the paste formulation as hydrogels appeared to be too loose to ensure lasting scaffolding properties. On the contrary, packing of the granules during the application of paste reduced biomaterial degradation rate and prevent the penetration of newly vascularized tissue, thus impeding grafting of split-thickness autologous skin grafts on the dermal substitute base.

  19. Pre-clinical evaluation of soybean-based wound dressings and dermal substitute formulations in pig healing and non-healing in vivo models.

    Shevchenko, Rostislav V; Santin, Matteo

    2014-01-01

    In the last decade, a new class of natural biomaterials derived from de-fatted soybean flour processed by either thermoset or extraction procedures has been developed. These biomaterials uniquely combine adaptability to various clinical applications to proven tissue regeneration properties. In the present work, the biomaterials were formulated either as hydrogel or as paste formulation and their potential as wound dressing material or as dermal substitute was assessed by two in vivo models in pig skin: The healing full-thickness punch biopsy model and the non-healing full-thickness polytetrafluoroethylene (PTFE) chamber model. The results clearly show that collagen deposition is induced by the presence of these biomaterials. A unique pattern of early inflammatory response, eliciting neutrophils and controlling macrophage infiltration, is followed by tissue cell colonization of the wound bed with a significant deposition of collagen fibers. The study also highlighted the importance in the use of optimal formulations and appropriate handling upon implantation. In large size, non-healing wounds, wound dermis was best obtained with the paste formulation as hydrogels appeared to be too loose to ensure lasting scaffolding properties. On the contrary, packing of the granules during the application of paste reduced biomaterial degradation rate and prevent the penetration of newly vascularized tissue, thus impeding grafting of split-thickness autologous skin grafts on the dermal substitute base.

  20. Experimental and kinetic modelling studies on the acid-catalysed hydrolysis of the water hyacinth plant to levulinic acid

    Girisuta, B.; Danon, B.; Manurung, R.; Janssen, L. P. B. M.; Heeres, H. J.

    2008-01-01

    A comprehensive experimental and modelling study on the acid-catalysed hydrolysis of the water hyacinth plant (Eichhornia crassipes) to optimise the yield of levulinic acid (LA) is reported (T = 150-175 degrees C, C-H2SO4 - 0.1-1 M, water hyacinth intake = 1-5 wt%). At high acid concentrations (> 0.

  1. Metabotyping of docosahexaenoic acid - treated Alzheimer's disease cell model.

    Priti Bahety

    Full Text Available BACKGROUND: Despite the significant amount of work being carried out to investigate the therapeutic potential of docosahexaenoic acid (DHA in Alzheimer's disease (AD, the mechanism by which DHA affects amyloid-β precursor protein (AβPP-induced metabolic changes has not been studied. OBJECTIVE: To elucidate the metabolic phenotypes (metabotypes associated with DHA therapy via metabonomic profiling of an AD cell model using gas chromatography time-of-flight mass spectrometry (GC/TOFMS. METHODS: The lysate and supernatant samples of CHO-wt and CHO-AβPP695 cells treated with DHA and vehicle control were collected and prepared for GC/TOFMS metabonomics profiling. The metabolic profiles were analyzed by multivariate data analysis techniques using SIMCA-P+ software. RESULTS: Both principal component analysis and subsequent partial least squares discriminant analysis revealed distinct metabolites associated with the DHA-treated and control groups. A list of statistically significant marker metabolites that characterized the metabotypes associated with DHA treatment was further identified. Increased levels of succinic acid, citric acid, malic acid and glycine and decreased levels of zymosterol, cholestadiene and arachidonic acid correlated with DHA treatment effect. DHA levels were also found to be increased upon treatment. CONCLUSION: Our study shows that DHA plays a role in mitigating AβPP-induced impairment in energy metabolism and inflammation by acting on tricarboxylic acid cycle, cholesterol biosynthesis pathway and fatty acid metabolism. The perturbations of these metabolic pathways by DHA in CHO-wt and CHO-AβPP695 cells shed further mechanistic insights on its neuroprotective actions.

  2. Characterizing PUF disk passive air samplers for alkyl-substituted PAHs: Measured and modelled PUF-AIR partition coefficients with COSMO-RS.

    Parnis, J Mark; Eng, Anita; Mackay, Donald; Harner, Tom

    2016-02-01

    Isomers of alkyl-substituted polycyclic aromatic hydrocarbons (PAHs) and dibenzothiophenes are modelled with COSMO-RS theory to determine the effectiveness and accuracy of this approach for estimation of isomer-specific partition coefficients between air and polyurethane foam (PUF), i.e., KPUF-AIR. Isomer-specific equilibrium partitioning coefficients for a series of 23 unsubstituted and isomeric alkyl-substituted PAHs and dibenzothiophenes were measured at 22 °C. This data was used to determine the accuracy of estimated values using COSMO-RS, which is isomer specific, and the Global Atmospheric Passive Sampling (GAPS) template approach, which treats all alkyl-substitutions as a single species of a given side-chain carbon number. A recently developed oligomer-based model for PUF was employed, which consisted of a 1:1 condensed pair of 2,4-toluene-diisocyanide and glycerol. The COSMO-RS approach resulted in a significant reduction in the RMS error associated with simple PAHs and dibenzothiophene compared with the GAPS template approach. When used with alkylated PAHs and dibenzothiophenes grouped into carbon-number categories, the GAPS template approach gave lower RMS error (0.72) compared to the COSMO-RS result (0.87) when the latter estimates were averaged within the carbon-number-based categories. When the isomer-specific experimental results were used, the COSMO-RS approach resulted in a 21% reduction in RMS error with respect to the GAPS template approach, with a 0.57 RMS error for all alkylated PAHs and dibenzothiophenes studied. The results demonstrate that COSMO-RS theory is effective in generating isomer-specific PUF-air partition coefficients, supporting the application of PUF-based passive samplers for monitoring and research studies of polycyclic aromatic compounds (PACs) in air.

  3. Towards Sustainable Aquafeeds: Complete Substitution of Fish Oil with Marine Microalga Schizochytrium sp. Improves Growth and Fatty Acid Deposition in Juvenile Nile Tilapia (Oreochromis niloticus).

    Sarker, Pallab K; Kapuscinski, Anne R; Lanois, Alison J; Livesey, Erin D; Bernhard, Katie P; Coley, Mariah L

    2016-01-01

    We conducted a 84-day nutritional feeding experiment with dried whole cells of DHA-rich marine microalga Schizochytrium sp. (Sc) to determine the optimum level of fish-oil substitution (partial or complete) for maximum growth of Nile tilapia. When we fully replaced fish oil with Schizochytrium (Sc100 diet), we found significantly higher weight gain and protein efficiency ratio (PER), and lower (improved) feed conversion ratio (FCR) and feed intake compared to a control diet containing fish oil (Sc0); and no significant change in SGR and survival rate among all diets. The Sc100 diet had the highest contents of 22:6n3 DHA, led to the highest DHA content in fillets, and consequently led to the highest DHA:EPA ratios in tilapia fillets. Schizochytrium sp. is a high quality candidate for complete substitution of fish oil in juvenile Nile tilapia feeds, providing an innovative means to formulate and optimize the composition of tilapia juvenile feed while simultaneously raising feed efficiency of tilapia aquaculture and to further develop environmentally and socially sustainable aquafeeds. Results show that replacing fish oil with DHA-rich marine Sc improves the deposition of n3 LC PUFA levels in tilapia fillet. These results support further studies to lower Schizochytrium production costs and to combine different marine microalgae to replace fish oil and fishmeal into aquafeeds.

  4. Towards Sustainable Aquafeeds: Complete Substitution of Fish Oil with Marine Microalga Schizochytrium sp. Improves Growth and Fatty Acid Deposition in Juvenile Nile Tilapia (Oreochromis niloticus)

    Sarker, Pallab K.; Kapuscinski, Anne R.; Lanois, Alison J.; Livesey, Erin D.; Bernhard, Katie P.; Coley, Mariah L.

    2016-01-01

    We conducted a 84-day nutritional feeding experiment with dried whole cells of DHA-rich marine microalga Schizochytrium sp. (Sc) to determine the optimum level of fish-oil substitution (partial or complete) for maximum growth of Nile tilapia. When we fully replaced fish oil with Schizochytrium (Sc100 diet), we found significantly higher weight gain and protein efficiency ratio (PER), and lower (improved) feed conversion ratio (FCR) and feed intake compared to a control diet containing fish oil (Sc0); and no significant change in SGR and survival rate among all diets. The Sc100 diet had the highest contents of 22:6n3 DHA, led to the highest DHA content in fillets, and consequently led to the highest DHA:EPA ratios in tilapia fillets. Schizochytrium sp. is a high quality candidate for complete substitution of fish oil in juvenile Nile tilapia feeds, providing an innovative means to formulate and optimize the composition of tilapia juvenile feed while simultaneously raising feed efficiency of tilapia aquaculture and to further develop environmentally and socially sustainable aquafeeds. Results show that replacing fish oil with DHA-rich marine Sc improves the deposition of n3 LC PUFA levels in tilapia fillet. These results support further studies to lower Schizochytrium production costs and to combine different marine microalgae to replace fish oil and fishmeal into aquafeeds. PMID:27258552

  5. Towards Sustainable Aquafeeds: Complete Substitution of Fish Oil with Marine Microalga Schizochytrium sp. Improves Growth and Fatty Acid Deposition in Juvenile Nile Tilapia (Oreochromis niloticus.

    Pallab K Sarker

    Full Text Available We conducted a 84-day nutritional feeding experiment with dried whole cells of DHA-rich marine microalga Schizochytrium sp. (Sc to determine the optimum level of fish-oil substitution (partial or complete for maximum growth of Nile tilapia. When we fully replaced fish oil with Schizochytrium (Sc100 diet, we found significantly higher weight gain and protein efficiency ratio (PER, and lower (improved feed conversion ratio (FCR and feed intake compared to a control diet containing fish oil (Sc0; and no significant change in SGR and survival rate among all diets. The Sc100 diet had the highest contents of 22:6n3 DHA, led to the highest DHA content in fillets, and consequently led to the highest DHA:EPA ratios in tilapia fillets. Schizochytrium sp. is a high quality candidate for complete substitution of fish oil in juvenile Nile tilapia feeds, providing an innovative means to formulate and optimize the composition of tilapia juvenile feed while simultaneously raising feed efficiency of tilapia aquaculture and to further develop environmentally and socially sustainable aquafeeds. Results show that replacing fish oil with DHA-rich marine Sc improves the deposition of n3 LC PUFA levels in tilapia fillet. These results support further studies to lower Schizochytrium production costs and to combine different marine microalgae to replace fish oil and fishmeal into aquafeeds.

  6. Model for acid-base chemistry in nanoparticle growth (MABNAG

    T. Yli-Juuti

    2013-03-01

    Full Text Available Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapors condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapor pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapor pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3–20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm−3 for the sum of the bases. The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics

  7. Acid-base properties of 2:1 clays. I. Modeling the role of electrostatics.

    Delhorme, Maxime; Labbez, Christophe; Caillet, Céline; Thomas, Fabien

    2010-06-15

    We present a theoretical investigation of the titratable charge of clays with various structural charge (sigma(b)): pyrophyllite (sigma(b) = 0 e x nm(-2)), montmorillonite (sigma(b) = -0.7 e x nm(-2)) and illite (sigma(b) = -1.2 e x nm(-2)). The calculations were carried out using a Monte Carlo method in the Grand Canonical ensemble and in the framework of the primitive model. The clay particle was modeled as a perfect hexagonal platelet, with an "ideal" crystal structure. The only fitting parameters used are the intrinsic equilibrium constants (pK(0)) for the protonation/deprotonation reactions of the broken-bond sites on the lateral faces of the clay particles, silanol, =SiO(-) + H(+) --> =SiOH, and aluminol, =AlO(-1/2) + H(+) --> =AlOH(+1/2). Simulations are found to give a satisfactory description of the acid-base titration of montmorillonite without any additional fitting parameter. In particular, combining the electrostatics from the crystal substitutions with ionization constants, the simulations satisfactorily catch the shift in the titration curve of montmorillonite according to the ionic strength. Change in the ionic strength modulates the screening of the electrostatic interactions which results in this shift. Accordingly, the PZNPC is found to shift toward alkaline pH upon increasing the permanent basal charge. Unlike previous mean field model results, a significant decrease in PZNPC values is predicted in response to stack formation. Finally, the mean field approach is shown to be inappropriate to study the acid-base properties of clays.

  8. 允许重新进货情况下单周期可替代产品的库存模型%Single-period Two-product Inventory Model with Reorder and Substitution

    李小申; 高克权

    2006-01-01

    In market, excess demands for many products can be met by reorder even during one period, and retailers usually adopt substitution strategy for more benefit. Under the retailer's substitution strategy and permission of reorder, we develop the profits maximization model for the two-substitutable-product inventory problem with stochastic demands and proportional costs and revenues. We show that the objective function is concave and submodular, and therefore the optimal policy exists. We present the optimal conditions for order quantity and provide some properties of the optimal order quantities. Comparing our model with Netessine and Rudi's, we prove that reorder and adoption of the substitution strategy can raise the general profits and adjust down the general stock level.

  9. Effects of Ascorbic Acid, Phytic Acid and Tannic Acid on Iron Bioavailability from Reconstituted Ferritin Measured by an In Vitro Digestion/Caco-2 Cell Model

    The effects of ascorbic acid, phytate and tannic acid on Fe bioavailability from Fe supplied as ferritin was compared to FeSO4 using an in vitro digestion/Caco-2 cell model. Horse spleen ferritin (HSF) was chemically reconstituted into a plant-type ferritin (P-HSF). In the presence of ascorbic acid...

  10. Do carboximide–carboxylic acid combinations form co-crystals? The role of hydroxyl substitution on the formation of co-crystals and eutectics

    Ramanpreet Kaur

    2015-05-01

    Full Text Available Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular interactions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co-crystals or eutectics for the studied carboxylic acid/imide combinations.

  11. Do carboximide-carboxylic acid combinations form co-crystals? The role of hydroxyl substitution on the formation of co-crystals and eutectics.

    Kaur, Ramanpreet; Gautam, Raj; Cherukuvada, Suryanarayan; Guru Row, Tayur N

    2015-05-01

    Carboxylic acids, amides and imides are key organic systems which provide understanding of molecular recognition and binding phenomena important in biological and pharmaceutical settings. In this context, studies of their mutual interactions and compatibility through co-crystallization may pave the way for greater understanding and new applications of their combinations. Extensive co-crystallization studies are available for carboxylic acid/amide combinations, but only a few examples of carboxylic acid/imide co-crystals are currently observed in the literature. The non-formation of co-crystals for carboxylic acid/imide combinations has previously been rationalized, based on steric and computed stability factors. In the light of the growing awareness of eutectic mixtures as an alternative outcome in co-crystallization experiments, the nature of various benzoic acid/cyclic imide combinations is established in this paper. Since an additional functional group can provide sites for new intermolecular inter-actions and, potentially, promote supramolecular growth into a co-crystal, benzoic acids decorated with one or more hydroxyl groups have been systematically screened for co-crystallization with one unsaturated and two saturated cyclic imides. The facile formation of an abundant number of hydroxybenzoic acid/cyclic carboximide co-crystals is reported, including polymorphic and variable stoichiometry co-crystals. In the cases where co-crystals did not form, the combinations are shown invariably to result in eutectics. The presence or absence and geometric disposition of hydroxyl functionality on benzoic acid is thus found to drive the formation of co-crystals or eutectics for the studied carboxylic acid/imide combinations.

  12. Comparative acid-base properties of the surface of components of the CdTe-ZnS system in series of substitutional solid solutions and their analogs

    Kirovskaya, I. A.; Kasatova, I. Yu.

    2011-07-01

    The acid-base properties of the surface of solid solutions and binary components of the CdTe-ZnS system are studied by hydrolytic adsorption, nonaqueous conductometric titration, mechanochemistry, IR spectroscopy, and Raman scattering spectroscopy. The strength, nature, and concentration of acid centers on the original surface and that exposed to CO are determined. The changes in acid-base properties in dependence on the composition of the system under investigation in the series of CdB6, ZnB6 analogs are studied.

  13. 40 CFR 721.8780 - Substituted pyridine azo substituted phenyl.

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Substituted pyridine azo substituted... Specific Chemical Substances § 721.8780 Substituted pyridine azo substituted phenyl. (a) Chemical substance... substituted pyridine azo substituted phenyl (PMNs P-96-767 and P-96-773) are subject to reporting under...

  14. Les substitutions énergétiques dans le secteur industriel français : la modélisation translog Energy Substitutions in the French Industrial Sector: Translog Modeling

    Le Roux Y.

    2006-11-01

    Full Text Available Les auteurs étudient dans cet article la structure de la demande d'énergie du secteur industriel français de 1962 à1982. Le modèle utilisé consiste à estimer l'effet des prix des 4 énergies : pétrole, gaz, électricité et charbon, sur la part de la facture énergétique correspondant à chacune de ces consommations. On mesure alors la substituabilité ou la complémentarité des énergies entre elles. Cet article comprend une partie théorique où est présentée la méthodologie retenue : l'approximation translog de la fonction de production, et une deuxième partie qui analyse les résultats obtenus pour le cas français. This article examines the structure of the energy demand by the French industrial sector from 1972 to 1982. The model used consists in estimating the effect of the price of four energy sources (oil, gas, electricity, coal on the share of the energy bill corresponding to the consumption of each energy source. Then the substitutability or complementarity of the energy sources among each other is measured. This article includes a theoretical part describing the methodology chosen. This methodology is the translog approximation of the production function. It also includes a second part which analyzes the results obtained for the case of France.

  15. Design, synthesis and in vitro evaluation of a series of α-substituted phenylpropanoic acid PPARγ agonists to further investigate the stereochemistry-activity relationship.

    Ohashi, Masao; Nakagome, Izumi; Kasuga, Jun-Ichi; Nobusada, Hiromi; Matsuno, Kenji; Makishima, Makoto; Hirono, Shuichi; Hashimoto, Yuichi; Miyachi, Hiroyuki

    2012-11-01

    We previously demonstrated that the α-benzylphenylpropanoic acid-type PPARγ-selective agonist 6 exhibited a reversed stereochemistry-activity relationship, that is, the (R)-enantiomer is a more potent PPARγ agonist than the (S)-enantiomer, compared with structurally similar α-ethylphenylpropanoic acid-type PPAR agonists. Here, we designed, synthesized and evaluated the optically active α-cyclohexylmethylphenylpropanoic acid derivatives 7 and α-phenethylphenylpropanoic acid derivatives 8, respectively. Interestingly, α-cyclohexylmethyl derivatives showed reversal of the stereochemistry-activity relationship [i.e., (R) more potent than (S)], like α-benzyl derivatives, whereas α-phenethyl derivatives showed the 'normal' relationship [(S) more potent than (R)]. These results suggested that the presence of a branched carbon atom at the β-position with respect to the carboxyl group is a critical determinant of the reversed stereochemistry-activity relationship.

  16. Model for acid-base chemistry in nanoparticle growth (MABNAG)

    Yli-Juuti, T.; Barsanti, K.; Hildebrandt Ruiz, L.; Kieloaho, A.-J.; Makkonen, U.; Petäjä, T.; Ruuskanen, T.; Kulmala, M.; Riipinen, I.

    2013-12-01

    Climatic effects of newly-formed atmospheric secondary aerosol particles are to a large extent determined by their condensational growth rates. However, all the vapours condensing on atmospheric nanoparticles and growing them to climatically relevant sizes are not identified yet and the effects of particle phase processes on particle growth rates are poorly known. Besides sulfuric acid, organic compounds are known to contribute significantly to atmospheric nanoparticle growth. In this study a particle growth model MABNAG (Model for Acid-Base chemistry in NAnoparticle Growth) was developed to study the effect of salt formation on nanoparticle growth, which has been proposed as a potential mechanism lowering the equilibrium vapour pressures of organic compounds through dissociation in the particle phase and thus preventing their evaporation. MABNAG is a model for monodisperse aqueous particles and it couples dynamics of condensation to particle phase chemistry. Non-zero equilibrium vapour pressures, with both size and composition dependence, are considered for condensation. The model was applied for atmospherically relevant systems with sulfuric acid, one organic acid, ammonia, one amine and water in the gas phase allowed to condense on 3-20 nm particles. The effect of dissociation of the organic acid was found to be small under ambient conditions typical for a boreal forest site, but considerable for base-rich environments (gas phase concentrations of about 1010 cm-3 for the sum of the bases). The contribution of the bases to particle mass decreased as particle size increased, except at very high gas phase concentrations of the bases. The relative importance of amine versus ammonia did not change significantly as a function of particle size. While our results give a reasonable first estimate on the maximum contribution of salt formation to nanoparticle growth, further studies on, e.g. the thermodynamic properties of the atmospheric organics, concentrations of low

  17. Tax Rates as Strategic Substitutes

    R.A. de Mooij (Ruud); H. Vrijburg (Hendrik)

    2012-01-01

    textabstractThis paper analytically derives the conditions under which the slope of the tax reaction function is negative in a classical tax competition model. If countries maximize welfare, we show that a negative slope (reflecting strategic substitutability) occurs under relatively mild conditions

  18. Tax rates as strategic substitutes

    H. Vrijburg (Hendrik); R.A. de Mooij (Ruud)

    2016-01-01

    textabstractThis paper analytically derives conditions under which the slope of the tax-reaction function is negative in a classical tax competition model. If countries maximize welfare, a negative slope (reflecting strategic substitutability) occurs under relatively mild conditions. The strategic t

  19. Comparison of three calcium phosphate bone graft substitutes from biomechanical, histological, and crystallographic perspectives using a rat posterolateral lumbar fusion model.

    Hu, Ming-Hsien; Lee, Pei-Yuan; Chen, Wen-Cheng; Hu, Jin-Jia

    2014-12-01

    This study evaluated the effectiveness of three calcium phosphate bone graft substitutes with different chemical compositions on spinal fusion using a rat posterolateral lumbar fusion model. Specifically, two recently developed non-dispersive tetracalcium phosphate/dicalcium phosphate anhydrous-based calcium phosphate cements (CPCs), namely a CPC consisting of equimolar amounts of the two compounds (nd-CPC) and a CPC consisting of a two-fold greater amount of dicalcium phosphate anhydrous (DCP-rich CPC), were compared with a commercial calcium phosphate bone graft (c-CPG) consisting of hydroxyapatite (60%) and β-tricalcium phosphate (40%). Single-level posterolateral lumbar fusion was performed at the L4-L5 vertebrae in fifteen adult rats (n=5 for each group). Spinal fusion was evaluated with radiographs, manual palpation, mechanical testing, micro-CT, and histology 8 weeks post-surgery. In particular, the crystallographic phases in the three substitutes were identified before and 8 weeks after their implantation. Manual palpation revealed stable constructs in nearly all of the spine specimens. The stiffness and bending load of fused spines in the two CPC groups were comparable to those in the c-CPG group. The radiographs specifically revealed implant resorption and bone remodeling in the DCP-rich CPC group. Analysis of 3D micro-CT images revealed that the bone volume ratio in the DCP-rich CPC group was significantly greater than those in the nd-CPC and c-CPG groups. Histology showed that the DCP-rich CPC group exhibited the highest degree of bone regeneration and osseointegration. Notably, DCP-rich CPC led to a pronounced phase transformation, generating the greatest amount of poorly crystalline apatite among the three groups, which together with adequate resorption may explain the aforementioned positive findings. We therefore conclude that of the bone graft substitutes considered, DCP-rich CPC has the greatest potential to be used in spinal fusion.

  20. Trypanosoma brucei gambiense group 1 is distinguished by a unique amino acid substitution in the HpHb receptor implicated in human serum resistance.

    Rebecca E Symula

    Full Text Available Trypanosoma brucei rhodesiense (Tbr and T. b. gambiense (Tbg, causative agents of Human African Trypanosomiasis (sleeping sickness in Africa, have evolved alternative mechanisms of resisting the activity of trypanosome lytic factors (TLFs, components of innate immunity in human serum that protect against infection by other African trypanosomes. In Tbr, lytic activity is suppressed by the Tbr-specific serum-resistance associated (SRA protein. The mechanism in Tbg is less well understood but has been hypothesized to involve altered activity and expression of haptoglobin haemoglobin receptor (HpHbR. HpHbR has been shown to facilitate internalization of TLF-1 in T.b. brucei (Tbb, a member of the T. brucei species complex that is susceptible to human serum. By evaluating the genetic variability of HpHbR in a comprehensive geographical and taxonomic context, we show that a single substitution that replaces leucine with serine at position 210 is conserved in the most widespread form of Tbg (Tbg group 1 and not found in related taxa, which are either human serum susceptible (Tbb or known to resist lysis via an alternative mechanism (Tbr and Tbg group 2. We hypothesize that this single substitution contributes to reduced uptake of TLF and thus may play a key role in conferring serum resistance to Tbg group 1. In contrast, similarity in HpHbR sequence among isolates of Tbg group 2 and Tbb/Tbr provides further evidence that human serum resistance in Tbg group 2 is likely independent of HpHbR function.

  1. [The role of some individual amino acid substitutions in penicillin-binding protein (PBP2) of Neisseria gonorrhoeae in the emergence of resistance to ceftriaxone].

    Kubanova, A A; Kubanov, A A; Kozhushnaia, O S; Vorob'ev, D V; Solomka, V S; Frigo, N V

    2014-01-01

    The goal of the study was to identify amino acid replacements in the structure of penicillin-binding protein PBP2, which may influence on the development of resistance N. gonorhoeae to the III cephalosporins generation. The gene penA of 50 strains of N. gonorrhoeae was sequenced: 20 strains with high sensitivity to ceftriaxone (MIC, Minimum Inhibitory Concentration, = 0.002 mg/L) and 30 strains with decreased sensitivity to ceftriaxone (MIC = 0.03-0.25 mg/L). The difference of MIC sensitivity between these strains was 30-250 times. Then nucleotide sequence was transformed into the amino acid sequence of PBP2 protein. Mutations in the gene penA and amino acid replacements in the protein PBP2 were found in 16 of 20 strains (80%) with high sensitivity to ceftriaxone and in all strains with decreased sensitivity to ceftriaxone. Amino acid replacements in the PBP2 protein were compared with amino acid replacements in groups, which characterize the PBP2 structure in accordance with the international classification Ito M. The amino acid replacement of PBP2 at positions 346, 505, 511, 517, 543, 567, 575, 576 are associated with V group by Ito M and have features of resistance of N. gonorrhoeae to ceftriaxone authentically (OR = 3.9 ± 2.5; χ2 = 4.9; p gonorrhoeae strains to ceftriaxone.

  2. Synthesis, structure, antitumor activity of novel pharmaceutical co-crystals based on bispyridyl-substituted α, β-unsaturated ketones with gallic acid

    Liu, Lian-Dong; Liu, Shu-Lian; Liu, Zhi-Xian; Hou, Gui-Ge

    2016-05-01

    Three novel pharmaceutical co-crystals, (A)·(gallic acid) (1), (B)·(gallic acid) (2), and (C)·(gallic acid) (3) were generated based on 2,6-bis((pyridin-4-yl)methylene)cyclohexanone (A), N-methyl-3,5-bis((pyridin-3-yl)methylene)-4-piperidone (B), N-methyl-3,5-bis((pyridin-4-yl)methylene)-4-piperidone (C) with gallic acid, respectively. They are characterized by elemental analysis, FTIR spectroscopy, 1H NMR and single-crystal X-ray diffraction. Structural analysis reveals that two pharmaceutical ingredients link each other into H-bonding-driven 3D network in 1, 2, or 2D plane in 3. In addition, their antitumor activities against human neoplastic cell lines A549, SGC-7901, MCF-7, OVCA-433, HePG2 and cytotoxicity for HUVEC cell lines by CCK-8 method were evaluated primarily. Compared with gallic acid and free A, B and C, their antitumor activities have improved distinctly, while cytotoxicities have reduced markedly, especially for co-crystal 1. This is mainly because of the synergistic effect between pharmaceutical ingredients A, B, and C and gallic acid.

  3. Mouse model of ulcerative colitis using trinitrobenzene sulfonic acid

    Irfan Ahmad Rather

    2015-12-01

    Full Text Available Animal model of intestinal inflammation is of paramount significance that aids in discerning the pathologies underlying ulcerative colitis and Crohn’s disease, the two clinical presentations of inflammatory bowel disease. The 2,4,6-trinitrobenzene sulfonic acid (TNBS colitis model represents one such intestinal inflammation-prototype that is generated in susceptible strains of mice through intra-rectal instillation of compound TNBS. In this paper, we demonstrate the experimental induction of TNBS-mediated colitis in a susceptible strain of ICR mice. This can be done by the following steps: a acclimation, b induction and c observation. TNBS-mouse model provides the information in shortest possible time and simultaneously represents a cost effective and highly reproducible model method of studying the pathogenesis of inflammatory bowel disease.

  4. Modelling of acid mine drainage (AMD in columns

    C. M. Bernardes de Souza

    2011-09-01

    Full Text Available A model is proposed in this paper to describe the generation of acid mine drainage (AMD in leaching columns. The model considers: (i Water flow through the column, which is calculated using the 1 - D analytic solution of the Richards' equation assuming the existence of a similarity relationship between the water retention function and the water content profiles at a given time; and (ii Pyrite oxidation weighted by microbiological effects occurring in spherical particles according to the shrinking core model. Mass balances of oxygen and pyrite were derived in order to evaluate the intrinsic oxidation rate and the pyrite fraction reacted with time and column position. The model was used to simulate a six month operation of a leaching column, which comprised successive weekly cycles of dry and wet periods. Simulation results demonstrated that AMD generation is strongly affected by the presence of microorganisms. A relative deviation of 5% between simulation and experimental data was obtained.

  5. Effects of organic acids, amino acids and ethanol on the radio-degradation of patulin in an aqueous model system

    Yun, Hyejeong [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Chonbuk, Jeongeup 580-185 (Korea, Republic of); Department of Food Science and Technology, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Lim, Sangyong [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Chonbuk, Jeongeup 580-185 (Korea, Republic of); Jo, Cheorun [Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Chung, Jinwoo [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Chonbuk, Jeongeup 580-185 (Korea, Republic of); Kim, Soohyun [Glycomics Team, Korea Basic Science Institute, Daejeon 305-333 (Korea, Republic of); Kwon, Joong-Ho [Department of Food Science and Technology, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Kim, Dongho [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Chonbuk, Jeongeup 580-185 (Korea, Republic of)], E-mail: fungikim@kaeri.re.kr

    2008-06-15

    The effects of organic acids, amino acids, and ethanol on the radio-degradation of patulin by gamma irradiation in an aqueous model system were investigated. The patulin, dissolved in distilled water at a concentration of 50 ppm, was practically degraded by the gamma irradiation at the dose of 1.0 kGy, while 33% of the patulin remained in apple juice. In the aqueous model system, the radio-degradation of patulin was partially inhibited by the addition of organic acids, amino acids, and ethanol. The proportions of remaining patulin after irradiation with the dose of 1.0 kGy in the 1% solution of malic acid, citric acid, lactic acid, acetic acid, ascorbic acid, and ethanol were 31.4%, 2.3%, 31.2%, 6.1%, 50.8%, and 12.5%, respectively. During 30 days of storage, the remaining patulin was reduced gradually in the solution of ascorbic acid and malic acid compared to being stable in other samples. The amino acids, serine, threonine, and histidine, inhibited the radio-degradation of patulin. In conclusion, it was suggested that 1 kGy of gamma irradiation (recommended radiation doses for radicidation and/or quarantine in fruits) is effective for the reduction of patulin, but the nutritional elements should be considered because the radio-degradation effects are environment dependent.

  6. Comparison of three calcium phosphate bone graft substitutes from biomechanical, histological, and crystallographic perspectives using a rat posterolateral lumbar fusion model

    Hu, Ming-Hsien [Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (China); Department of Orthopedics, Show-Chwan Memorial Hospital, Changhua 50544, Taiwan (China); Department of Orthopedic Surgery, Faculty of Medicine, National Yang-Ming University, Taipei 112, Taiwan (China); Lee, Pei-Yuan [Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (China); Department of Orthopedics, Show-Chwan Memorial Hospital, Changhua 50544, Taiwan (China); Chen, Wen-Cheng, E-mail: wincheng0925@yahoo.com.tw [Department of Fiber and Composite Materials, College of Engineering, Feng Chia University, Taichung 40724, Taiwan (China); Hu, Jin-Jia, E-mail: jjhu@mail.ncku.edu.tw [Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan (China); Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan (China)

    2014-12-01

    This study evaluated the effectiveness of three calcium phosphate bone graft substitutes with different chemical compositions on spinal fusion using a rat posterolateral lumbar fusion model. Specifically, two recently developed non-dispersive tetracalcium phosphate/dicalcium phosphate anhydrous-based calcium phosphate cements (CPCs), namely a CPC consisting of equimolar amounts of the two compounds (nd-CPC) and a CPC consisting of a two-fold greater amount of dicalcium phosphate anhydrous (DCP-rich CPC), were compared with a commercial calcium phosphate bone graft (c-CPG) consisting of hydroxyapatite (60%) and β-tricalcium phosphate (40%). Single-level posterolateral lumbar fusion was performed at the L4–L5 vertebrae in fifteen adult rats (n = 5 for each group). Spinal fusion was evaluated with radiographs, manual palpation, mechanical testing, micro-CT, and histology 8 weeks post-surgery. In particular, the crystallographic phases in the three substitutes were identified before and 8 weeks after their implantation. Manual palpation revealed stable constructs in nearly all of the spine specimens. The stiffness and bending load of fused spines in the two CPC groups were comparable to those in the c-CPG group. The radiographs specifically revealed implant resorption and bone remodeling in the DCP-rich CPC group. Analysis of 3D micro-CT images revealed that the bone volume ratio in the DCP-rich CPC group was significantly greater than those in the nd-CPC and c-CPG groups. Histology showed that the DCP-rich CPC group exhibited the highest degree of bone regeneration and osseointegration. Notably, DCP-rich CPC led to a pronounced phase transformation, generating the greatest amount of poorly crystalline apatite among the three groups, which together with adequate resorption may explain the aforementioned positive findings. We therefore conclude that of the bone graft substitutes considered, DCP-rich CPC has the greatest potential to be used in spinal fusion

  7. A single amino acid substitution (Trp(666)-->Ala) in the interbox1/2 region of the interleukin-6 signal transducer gp130 abrogates binding of JAK1, and dominantly impairs signal transduction.

    Haan, C; Hermanns, H M; Heinrich, P C; Behrmann, I

    2000-07-01

    gp130 is the common signal-transducing receptor chain of interleukin (IL)-6-type cytokines. Here we describe, for the first time, a single amino acid substitution (Trp(666)-->Ala) in the membrane-proximal interbox1/2 region that abrogates activation of STAT (signal transducer and activator of transcription) transcription factors and the proliferative response of pro-B-cell transfectants. Moreover, association of the Janus kinase JAK1 is prevented. No signalling of heterodimeric IL-5 receptor (IL-5R)/gp130 chimaeras occurs in COS-7 cells, even when only a single cytoplasmic chain of a gp130 dimer contains the Trp(666)Ala mutation, indicating that it acts dominantly.

  8. Dynamics of cetyltrimethylammonium bromide mediated reaction of phenylsulfinylacetic acid with Cr(VI: Treatment of pseudo-phase models

    Subramaniam Perumal

    2015-01-01

    The influence of cetyltrimethylammonium bromide, CTon the oxidative decarboxylation of phenylsulfinylacetic acid, PSAA and several meta- and para-substituted PSAAs by Cr(VI was investigated in 95 % H2O-5 % CH3CN medium. The rate profile displayed a peculiar trend with an initial rate increase at low [CTAB] followed by sharp rate inhibition at higher [CTAB]. The initial rate acceleration can be explained by strong binding of SO42- on the positively charged micellar surface. The specific partitioning of PSAA in micellar phase by hydrophobic interaction and the oxidizing species, HCrO3+ in aqueous phase by electrostatic repulsion accounted the rate retardation at higher [CTAB]. The Hammett plot with different substituted PSAAs showed an excellent correlation affording negative ρ value which supports the proposed mechanism involving a sulfonium cation intermediate formation. The obtained ρ value in CTmedium is found to be slightly lower than that in aqueous medium. The quantitative analysis of rate data for the inhibition shown by CTwas performed using Menger-Portnoy and Piszkiewicz pseudo-phase models. The binding constant for PSAA with micelle was evaluated from Piszkiewicz cooperative model.

  9. Understanding atmospheric peroxyformic acid chemistry: observation, modeling and implication

    H. Liang

    2015-01-01

    Full Text Available The existence and importance of peroxyformic acid (PFA in the atmosphere has been under controversy. We present here, for the first time, the observation data for PFA from four field measurements carried out in China. These data provided powerful evidence that PFA can stay in the atmosphere, typically in dozens of pptv level. The relationship between PFA and other detected peroxides was examined. The results showed that PFA had a strong positive correlation with its homolog, peroxyacetic acid, due to their similar sources and sinks. Through an evaluation of PFA production and removal rates, we proposed that the reactions between peroxyformyl radical (HC(OO2 and formaldehyde or the hydroperoxyl radical (HO2 were likely to be the major source and degradation into formic acid (FA was likely to be the major sink for PFA. Based on a box model evaluation, we proposed that the HC(OO2 and PFA chemistry was a major source for FA under low NOx conditions. Furthermore, it is found that the impact of the HC(OO2 and PFA chemistry on radical cycling was dependent on the yield of HC(OO2 radical from HC(O + O2 reaction. When this yield exceeded 50%, the HC(OO2 and PFA chemistry should not be neglected for calculating the radical budget. To make clear the exact importance of HC(OO2 and PFA chemistry in the atmosphere, further kinetic, field and modeling studies are required.

  10. Kinetics and mechanism of the oxidation of some substituted aldonitrones by quinolinium chlorochromate in aqueous DMF medium in the absence and presence of oxalic acid

    GOVINDASAMY RAJARAJAN

    2009-02-01

    Full Text Available The kinetics of the oxidation of aldonitrones (nitrone by quinolinium chlorochromate (QCC was determined in 50 % DMF–water in the absence and presence of oxalic acid in order to study the effect of oxalic acid. It was considered worthwhile to investigate whether it undergoes co-oxidation or just functions as a catalyst in the reaction. The reaction was followed iodometrically. Under the employed experimental conditions, the reaction is first order each with respect to concentration of nitrone, QCC, and oxalic acid and fractional order with respect to H+ concentration. There was no discernible effect with increasing in ionic strength but the rate of oxidation decreased with decreasing dielectric constant of the medium. Addition of MnSO4 had a significant and acrylonitrile no effect on the reaction rate. A mechanism involving protonated nitrone and QCC as the reactive oxidant is proposed. The activation parameters were calculated and are presented.

  11. N-Terminal Fatty Acid Substitution Increases the Leishmanicidal Activity of CA(1-7)M(2-9), a Cecropin-Melittin Hybrid Peptide

    Chicharro, Cristina; Granata, Cesare; Lozano, Rosario; Andreu, David; Rivas, Luis

    2001-01-01

    In order to improve the leishmanicidal activity of the synthetic cecropin A-melittin hybrid peptide CA(1-7)M(2-9) (KWKLFKKIGAVLKVL-NH2), a systematic study of its acylation with saturated linear fatty acids was carried out. Acylation of the Nɛ-7 lysine residue led to a drastic decrease in leishmanicidal activity, whereas acylation at lysine 1, in either the α or the ɛ NH2 group, increased up to 3 times the activity of the peptide against promastigotes and increased up to 15 times the activity of the peptide against amastigotes. Leishmanicidal activity increased with the length of the fatty acid chain, reaching a maximum for the lauroyl analogue (12 carbons). According to the fast kinetics, dissipation of membrane potential, and parasite membrane permeability to the nucleic acid binding probe SYTOX green, the lethal mechanism was directly related to plasma membrane permeabilization. PMID:11502512

  12. Bile acid malabsorption or disturbed intestinal permeability in patients treated with enzyme substitution for exocrine pancreatic insufficiency is not caused by bacterial overgrowth

    Madsen, Jan Lysgård; Graff, Jesper; Philipsen, Else Kirstine;

    2003-01-01

    enzyme replacement therapy, were studied. The prevalence of bacterial overgrowth was evaluated by means of a hydrogen and methane breath test with glucose. Gamma camera scintigraphy after intake of 75Se-homocholic acid taurine (75Se-HCAT) was used to evaluate bile acid absorption capacity. Intestinal......INTRODUCTION: In some patients with severe exocrine pancreatic insufficiency, enzyme replacement therapy will not lead to clinical improvement or reduction of steatorrhea. Therefore, other mechanisms separately or in interplay with reduced enzyme secretion might be responsible for malabsorption...... in these patients. AIMS: To evaluate the prevalence of bacterial overgrowth, bile acid absorption capacity, and intestinal permeability in a group of patients with well-characterized exocrine pancreatic insufficiency. METHODOLOGY: Eleven men with severe exocrine pancreatic insufficiency, of whom 10 were receiving...

  13. The Effect of Opsteoporotic Model Rats Induced by Retinoic Acid

    Xu Peng; Yao Jianfeng; Jin Weizhang; Cai Qiankun; Guo Xiong

    2005-01-01

    Objective: To study the effect of retinoic acid on inducing osteoporosis in female rat. Methods: 48SD female rats were divided randomly into experiment group and control group. Retinoic acid was administered orally to experiment group with 80mg.kg-1d-1 for 15 days. Then the rats were sacrificed on the 0th, 30th, 60th days after last administration. The serum concentration of Ca, P, BGP, E2, AKP and TRAP were detected. Components of collagen and proteoglycan in the bones and BMD were also assayed .The femoral morphometric change and epiphyseal plate cartilage histological changes were observed. Results: After a 15-day period treatment with retinoic acid, charateristics of experiment group were compared with control, it is shown that the concentration of serum E2 and BGP declined, the activity of AKP and TRAP increased while BMP decreased, the bone mass of both spongy bone and cortical bone reduced, the number of spongy bone osteoclasts and their activity increased, number of epiphyseal plate chondrocyte reduced, cartilage hypertrophic zone displayed dyscalcification, and no difference of other markers was found in the two groups. On the 30th day after the last administration, the experiment group appeared a declined number of cancellous bone osteoclast and level of serum AKP yet they were still higher than control. Number of epiphyseal chondrocyte, serum BGP and tibial BMD, though higher than before, were still lower than control. Other markers were no difference. On the 60th day after treatment, although the femoral cancellous bone mass was still less and cancellous osteoblast was more than control, the cortical bone mass, cancellous osteoclast number and level of serum Ca and P were all remained no different between two groups.Conclusion: Retinoic acid possessed a better short-term effect than long-term effect. Cancellous bone loss lasted much longer than cortical bone and more obviously; the bone matrix in this osteoporosis model was able to repair itself

  14. Commercial formalin substitutes for histopathology

    Prentø, P; Lyon, H

    1997-01-01

    of protein and structural immobilization, quality of histology and cellular structure following routine dehydration and paraffin embedding, and performance as a fixative for immunohistochemistry. Furthermore, we evaluated the effects of the various fixatives on ultrastructure. Only buffered formalin......We compared the performance of six commercial fixatives proposed to be formalin substitutes with the performance of buffered formalin, Clarke's ethanol-acetic acid, and ethanol, using rat liver, small intestine, and kidney. We investigated the rate of penetration, mode of fixation, extent...... performed equally well on all tissues tested. While several of the commercial fixatives appeared to preserve liver tissue at 200x, the preservation of kidney, intestinal villi, and smooth muscle was unacceptable. Histological distortion, cell shrinkage and vacuolization were prominent when the substitutes...

  15. Smart Phones and their Substitutes

    Bødker, Mads; Gimpel, Gregory; Hedman, Jonas

    2009-01-01

    Drawing on data from a longitudinal field study, this paper investigates the influence of existing, better and stand-alone technology substitutes on the use of smart phones. By applying prospect theory, media richness theory, and business model literature, the purpose of this paper is to improve...... our understanding of the role of substitutes, device content fit issues, and implications for business models by asking the question: What is an effective business model to address the relationship between user preference and the fit of the smart phone and everyday task? The field study data suggest...... the need for business models to recognize that adoption decisions are reference-dependent and strongly influenced by the fit between task and smart phone....

  16. Medicineringsfejl ved generisk substitution

    Rölfing, Jan

    2012-01-01

    Generic substitution is a major cause of medical mistakes in the general population. Danish legislation obligates pharmacies to substitute prescribed medicine with the cheapest equivalent formulation, despite variations in product name, packaging, shape and colour. Consequently, medical mistakes ...... occur. Scientific evidence on the consequences of generic substitution is sparse. Call upon fellow health workers to report medical mistakes to the national entities and scientific peers, in order to increase awareness and scientific evidence about the problem....

  17. Oxygen reduction in acid media: effect of iron substitution by cobalt on heat-treated naphthalocyanine impregnations supported on preselected carbon blacks

    Biloul, A.; Contamin, O.; Scarbeck, G.; Savy, M.; Ham, van den D.; Riga, J.; Verbist, J.J.

    1992-01-01

    FeNPc(1.2) impregnations were investigated at various loadings using a rotating-disk electrode, voltammetry and X-ray photoelectron spectroscopy (XPS) techniques. Optimal activity takes place at monolayer coverage, and major demetallation occurs after prolonged exposure to acid solution. The substit

  18. Site-specific antibodies distinguish single amino acid substitutions in position 57 in HLA-DQ beta-chain alleles associated with insulin-dependent diabetes

    Atar, D; Dyrberg, T; Michelsen, Birgitte

    1989-01-01

    The HLA-DQ beta-chain gene shows a close association with susceptibility or resistance to autoimmune insulin-dependent diabetes mellitus (IDDM) and it has been suggested that the amino acid in position 57 may be of pathogenetic importance. To study the expression of the IDDM associated HLA-DQ beta......-chain alleles, we immunized rabbits with 12 to 13 amino acid long peptides representing HLA-DQw7 and -DQw8 allelic sequences, differing only by one amino acid in position 57 being aspartic acid (Asp) and alanine (Ala), respectively. Immunoblot analysis of lymphoblastoid cells showed that several antisera...... recognized a 29-kDa protein, equivalent to the expected molecular size of the HLA-DQ beta-chain to yield two antisera specific for HLA-DQw7 (pos. 57Asp) and three antisera for HLA-DQw8 (pos. 57Ala) positive cells. Analysis of HLA-DR 3/4 positive IDDM patients (n = 24) and controls (n = 19) showed that all...

  19. Modelling of Rare Earth Elements Complexation With Humic Acid

    Pourret, O.; Davranche, M.; Gruau, G.; Dia, A.

    2006-12-01

    The binding of rare earth elements (REE) to humic acid (HA) was studied by combining Ultrafiltration and ICP- MS techniques. REE-HA complexation experiments were performed at various pH conditions (ranging from 2 to 10.5) using a standard batch equilibration method. Results show that the amount of REE bound to HA strongly increase with increasing pH. Moreover, a Middle REE (MREE) downward concavity is evidenced by REE distribution patterns at acidic pH. Modelling of the experimental data using Humic Ion Binding Model VI provided a set of log KMA values (i.e. the REE-HA complexation constants specific to Model VI) for the entire REE series. The log KMA pattern obtained displays a MREE downward concavity. Log KMA values range from 2.42 to 2.79. These binding constants are in good agreement with the few existing datasets quantifying the binding of REE with humic substances except a recently published study which evidence a lanthanide contraction effect (i.e. continuous increase of the constant from La to Lu). The MREE downward concavity displayed by REE-HA complexation pattern determined in this study compares well with results from REE-fulvic acid (FA) and REE-acetic acid complexation studies. This similarity in the REE complexation pattern shapes suggests that carboxylic groups are the main binding sites of REE in HA. This conclusion is further supported by a detailed review of published studies for natural, organic-rich, river- and ground-waters which show no evidence of a lanthanide contraction effect in REE pattern shape. Finally, application of Model VI using the new, experimentally determined log KMA values to World Average River Water confirms earlier suggestions that REE occur predominantly as organic complexes (> 60 %) in the pH range between 5-5.5 and 7-8.5 (i.e. in circumneutral pH waters). The only significant difference as compared to earlier model predictions made using estimated log KMA values is that the experimentally determined log KMA values

  20. Impact of charged amino acid substitution in the transmembrane domain of L-alanine exporter, AlaE, of Escherichia coli on the L-alanine export.

    Kim, Seryoung; Ihara, Kohei; Katsube, Satoshi; Ando, Tasuke; Isogai, Emiko; Yoneyama, Hiroshi

    2017-01-01

    The Escherichia coli alaE gene encodes the L-alanine exporter, AlaE, that catalyzes active export of L-alanine using proton electrochemical potential. The transporter comprises only 149 amino acid residues and four predicted transmembrane domains (TMs), which contain three charged amino acid residues. The AlaE-deficient L-alanine non-metabolizing cells (ΔalaE cells) appeared hypersusceptible to L-alanyl-L-alanine showing a minimum inhibitory concentration (MIC) of 2.5 µg/ml for the dipeptide due to a toxic accumulation of L-alanine. To elucidate the mechanism by which AlaE exports L-alanine, we replaced charged amino acid residues in the TMs, glutamic acid-30 (TM-I), arginine-45 (TM-II), and aspartic acid-84 (TM-III) with their respective charge-conserved amino acid or a net neutral cysteine. The ΔalaE cells producing R45K or R45C appeared hypersusceptible to the dipeptide, indicating that arginine-45 is essential for AlaE activity. MIC of the dipeptide in the ΔalaE cells expressing E30D and E30C was 156 µg/ml and >10,000 µg/ml, respectively, thereby suggesting that a negative charge at this position is not essential. The ΔalaE cells expressing D84E or D84C showed an MIC >10,000 and 78 µg/ml, respectively, implying that a negative charge is required at this position. These results were generally consistent with that of the L-alanine accumulation experiments in intact cells. We therefore concluded that charged amino acid residues (R45 and D84) in the AlaE transmembrane domain play a pivotal role in L-alanine export. Replacement of three cysteine residues at C22, C28 (both in TM-I), and C135 (C-terminal region) with alanine showed only a marginal effect on L-alanine export.

  1. Studies on naturally occurring infectious bursal disease viruses suggest that a single amino acid substitution at position 253 in VP2 increases pathogenicity.

    Jackwood, D J; Sreedevi, B; LeFever, L J; Sommer-Wagner, S E

    2008-07-20

    Three classic IBDV strains were previously isolated from commercial layer chicken flocks and shown to be phylogenetically related to vaccine strains but pathogenic in susceptible chickens. In this study, their viral genomes were sequenced and compared to sequences of vaccines being used in those flocks. The vaccine strains examined were sequenced directly from the manufacturer and had identical genome segment B sequences. Compared to these vaccines, the GA-1, H-30 and CS-2-35 isolates each had one silent mutation in the gene that encodes VP1. Compared to the two vaccines used at the time CS-2-35 was isolated, the segment A sequence of CS-2-35 contained numerous nucleotide and amino acid mutations suggesting the CS-2-35 virus was not closely related to these vaccines. This virus however did have amino acid mutations in VP2 that are reported to be necessary for replication in cell culture and lacked two of the three amino acid mutations previously shown to be necessary for virulence. These data suggest that CS-2-35 was a descendant from an attenuated strain of IBDV. When the segment A genomic sequences of the GA-1 and H-30 viruses were compared to the vaccines being used in those flocks they were most closely related to the attenuated D78 vaccine strain. In genome segment A, three nucleotide mutations in GA-1 and four in H-30 were observed compared to the D78 classic vaccine. These nucleotide mutations caused one amino acid (H253N) change in the GA-1 virus and two amino acids (H253Q and G259D) were different in the H-30 virus. In addition, both the GA-1 and H-30 viruses had the amino acid G76 in VP2 that appears to be unique to the vaccine D78. The data suggest that GA-1 and H-30 are genetically related and have a common ancestor even though they were isolated from geographically distant flocks. The evidence also suggests that GA-1, H-30 and CS-2-35 could be reversions from attenuated vaccine viruses or by coincidence genetically resemble classic IBDV vaccines. It

  2. Cyclotomic Aperiodic Substitution Tilings

    Stefan Pautze

    2017-01-01

    Full Text Available The class of Cyclotomic Aperiodic Substitution Tilings (CASTs is introduced. Its vertices are supported on the 2 n -th cyclotomic field. It covers a wide range of known aperiodic substitution tilings of the plane with finite rotations. Substitution matrices and minimal inflation multipliers of CASTs are discussed as well as practical use cases to identify specimen with individual dihedral symmetry D n or D 2 n , i.e., the tiling contains an infinite number of patches of any size with dihedral symmetry D n or D 2 n only by iteration of substitution rules on a single tile.

  3. Model application for acid mine drainage treatment processes

    Nantaporn Noosai, Vineeth Vijayan, Khokiat Kengskool

    2014-01-01

    Full Text Available This paper presents the utilization of the geochemical model, PHREEQC, to investigate the chemical treatment system for Acid Mine Drainage (AMD prior to the discharge. The selected treatment system consists of treatment processes commonly used for AMD including settling pond, vertical flow pond (VFP and caustic soda pond were considered in this study. The use of geochemical model for the treatment process analysis enhances the understanding of the changes in AMD’s chemistry (precipitation, reduction of metals, etc. in each process, thus, the chemical requirements (i.e., CaCO3 and NaOH for the system and the system’s treatment efficiency can be determined. The selected treatment system showed that the final effluent meet the discharge standard. The utilization of geochemical model to investigate AMD treatment processes can assist in the process design.

  4. Modelling strategies for the industrial exploitation of lactic acid bacteria.

    Teusink, Bas; Smid, Eddy J

    2006-01-01

    Lactic acid bacteria (LAB) have a long tradition of use in the food industry, and the number and diversity of their applications has increased considerably over the years. Traditionally, process optimization for these applications involved both strain selection and trial and error. More recently, metabolic engineering has emerged as a discipline that focuses on the rational improvement of industrially useful strains. In the post-genomic era, metabolic engineering increasingly benefits from systems biology, an approach that combines mathematical modelling techniques with functional-genomics data to build models for biological interpretation and--ultimately--prediction. In this review, the industrial applications of LAB are mapped onto available global, genome-scale metabolic modelling techniques to evaluate the extent to which functional genomics and systems biology can live up to their industrial promise.

  5. Haloacetic acid and trihalomethane formation from the chlorination and bromination of aliphatic beta-dicarbonyl acid model compounds.

    Dickenson, Eric R V; Summers, R Scott; Croué, Jean-Philippe; Gallard, Hervé

    2008-05-01

    While it is known that resorcinol- and phenol-type aromatic structures within natural organic matter (NOM) react during drinking water chlorination to form trihalomethanes (THMs), limited studies have examined aliphatic-type structures as THM and haloacetic acid (HAA) precursors. A suite of aliphatic acid model compounds were chlorinated and brominated separately in controlled laboratory-scale batch experiments. Four and two beta-dicarbonyl acid compounds were found to be important precursors for the formation of THMs (chloroform and bromoform (71-91% mol/mol)), and dihaloacetic acids (DXAAs) (dichloroacetic acid and dibromoacetic acid (5-68% mol/mol)), respectively, after 24 h at pH 8. Based upon adsorbable organic halide formation, THMs and DXAAs, and to a lesser extent mono and trihaloacetic acids, were the majority (> 80%) of the byproducts produced for most of the aliphatic beta-dicarbonyl acid compounds. Aliphatic beta-diketone-acid-type and beta-keto-acid-type structures could be possible fast- and slow-reacting THM precursors, respectively, and aliphatic beta-keto-acid-type structures are possible slow-reacting DXAA precursors. Aliphatic beta-dicarbonyl acid moieties in natural organic matter, particularly in the hydrophilic fraction, could contribute to the significant formation of THMs and DXAAs observed after chlorination of natural waters.

  6. Interference effects from coexisting fatty acids on elaidic acid separation by fractionating crystallization: A model study

    Jala, Ram Chandra Reddy; Guo, Zheng; Bjerring, Thomas;

    2010-01-01

    A multi-stage temperature-programmed fractionating crystallization process was carried out to examine the effects of the presence of stearic acid (SA), oleic acid (OA), and linoleic acid (LA) on the separation of elaidic acid (EA). The results showed that the efficiency of fractionating crystalli......A multi-stage temperature-programmed fractionating crystallization process was carried out to examine the effects of the presence of stearic acid (SA), oleic acid (OA), and linoleic acid (LA) on the separation of elaidic acid (EA). The results showed that the efficiency of fractionating...

  7. 1,1-Difluoroethyl-substituted triazolothienopyrimidines as inhibitors of a human urea transport protein (UT-B): new analogs and binding model.

    Liu, Y; Esteva-Font, C; Yao, C; Phuan, P W; Verkman, A S; Anderson, M O

    2013-06-01

    The kidney urea transport protein UT-B is an attractive target for the development of small-molecule inhibitors with a novel diuretic ('urearetic') action. Previously, two compounds in the triazolothienopyrimidine scaffold (1a and 1c) were reported as UT-B inhibitors. Compound 1c incorporates a 1,1-difluoroethyl group, which affords improved microsomal stability when compared to the corresponding ethyl-substituted compound 1a. Here, a small focused library (4a-4f) was developed around lead inhibitor 1c to investigate the requirement of an amidine-linked thiophene in the inhibitor scaffold. Two compounds (4a and 4b) with nanomolar inhibitory potency (IC50≈40 nM) were synthesized. Computational docking of lead structure 1c and 4a-4f into a homology model of the UT-B cytoplasmic surface suggested binding with the core heterocycle buried deep into the hydrophobic pore region of the protein.

  8. Investigation of DC current models in Co2+ and Ti4+ substituted M-type BaCox Tix Fe(12-2x) O19 ferrite

    Bhikhan, Vikas; Singh, Charanjeet; Kaur, Rajneesh; Jaroszewski, Maciej; Bindra Narang, S.

    2015-12-01

    The static current density ( J)-electric field ( E) characteristics of BaCo x Ti x Fe(12-2 x)O19 ferrite compositions ( x = 0.1, 0.3, 0.5, 0.7, 0.9) have been investigated at an applied field from 0.003 kV/m to 4.98 kV/m at room temperature. Compositions x = 0.3, 0.5 and 0.7 exhibit ohmic behavior at low applied field and non-linear conduction is observed in compositions x = 0.1, 0.3, 0.7 and 0.9 at higher applied field. The various non-linear conduction models, associated with Schottky, Poole-Frenkel, Ionic Hopping and Space Charge Limited Current mechanisms, have been discussed. The large current density has been found at higher substitution.

  9. Field trial evaluation of the accumulation of omega-3 long chain polyunsaturated fatty acids in transgenic Camelina sativa: Making fish oil substitutes in plants

    Sarah Usher

    2015-12-01

    Full Text Available The global consumption of fish oils currently exceeds one million tonnes, with the natural de novo source of these important fatty acids forming the base of marine foodwebs. Here we describe the first field-based evaluation of a terrestrial source of these essential nutrients, synthesised in the seeds of transgenic Camelina sativa plants via the heterologous reconstitution of the omega-3 long chain polyunsaturated fatty acid biosynthetic pathway. Our data demonstrate the robust nature of this novel trait, and the feasibility of making fish oils in genetically modified crops. Moreover, to our knowledge, this is the most complex example of plant genetic engineering to undergo environmental release and field evaluation.

  10. Lauric acid-rich medium-chain triglycerides can substitute for other oils in cooking applications and may have limited pathogenicity

    McCarty, Mark F; DiNicolantonio, James J

    2016-01-01

    Recently, medium-chain triglycerides (MCTs) containing a large fraction of lauric acid (LA) (C12)—about 30%—have been introduced commercially for use in salad oils and in cooking applications. As compared to the long-chain fatty acids found in other cooking oils, the medium-chain fats in MCTs are far less likely to be stored in adipose tissue, do not give rise to ‘ectopic fat’ metabolites that promote insulin resistance and inflammation, and may be less likely to activate macrophages. When ingested, medium-chain fatty acids are rapidly oxidised in hepatic mitochondria; the resulting glut of acetyl-coenzyme A drives ketone body production and also provokes a thermogenic response. Hence, studies in animals and humans indicate that MCT ingestion is less obesogenic than comparable intakes of longer chain oils. Although LA tends to raise serum cholesterol, it has a more substantial impact on high density lipoprotein (HDL) than low density lipoprotein (LDL) in this regard, such that the ratio of total cholesterol to HDL cholesterol decreases. LA constitutes about 50% of the fatty acid content of coconut oil; south Asian and Oceanic societies which use coconut oil as their primary source of dietary fat tend to be at low cardiovascular risk. Since ketone bodies can exert neuroprotective effects, the moderate ketosis induced by regular MCT ingestion may have neuroprotective potential. As compared to traditional MCTs featuring C6–C10, laurate-rich MCTs are more feasible for use in moderate-temperature frying and tend to produce a lower but more sustained pattern of blood ketone elevation owing to the more gradual hepatic oxidation of ingested laurate. PMID:27547436

  11. Lauric acid-rich medium-chain triglycerides can substitute for other oils in cooking applications and may have limited pathogenicity.

    McCarty, Mark F; DiNicolantonio, James J

    2016-01-01

    Recently, medium-chain triglycerides (MCTs) containing a large fraction of lauric acid (LA) (C12)-about 30%-have been introduced commercially for use in salad oils and in cooking applications. As compared to the long-chain fatty acids found in other cooking oils, the medium-chain fats in MCTs are far less likely to be stored in adipose tissue, do not give rise to 'ectopic fat' metabolites that promote insulin resistance and inflammation, and may be less likely to activate macrophages. When ingested, medium-chain fatty acids are rapidly oxidised in hepatic mitochondria; the resulting glut of acetyl-coenzyme A drives ketone body production and also provokes a thermogenic response. Hence, studies in animals and humans indicate that MCT ingestion is less obesogenic than comparable intakes of longer chain oils. Although LA tends to raise serum cholesterol, it has a more substantial impact on high density lipoprotein (HDL) than low density lipoprotein (LDL) in this regard, such that the ratio of total cholesterol to HDL cholesterol decreases. LA constitutes about 50% of the fatty acid content of coconut oil; south Asian and Oceanic societies which use coconut oil as their primary source of dietary fat tend to be at low cardiovascular risk. Since ketone bodies can exert neuroprotective effects, the moderate ketosis induced by regular MCT ingestion may have neuroprotective potential. As compared to traditional MCTs featuring C6-C10, laurate-rich MCTs are more feasible for use in moderate-temperature frying and tend to produce a lower but more sustained pattern of blood ketone elevation owing to the more gradual hepatic oxidation of ingested laurate.

  12. Selective catalytic hydroalkylation and deoxygenation of substituted phenols to bicycloalkanes

    Zhao, Chen; Camaioni, Donald M.; Lercher, Johannes A.

    2012-04-01

    Phenol and substituted phenols are hydroalkylated and hydrodeoxygenated to bi-cycloalkanes in a tandem reaction over Pd nanoclusters supported on a large-pore molecular sieve HBEA at 473-523 K using water as solvent. The HBEA-supported Pd catalyst (metal-acid ratio: 1:22 mol/mol) optimally balances the competing rates of metal catalyzed hydrogenation as well as of solid acid-catalyzed dehydration and carbon-carbon coupling to combine hydrodeoxygenation and dimerization of phenol derivatives to C{sub 12}-C{sub 18} bicycloalkanes in a single reaction sequence. A detailed kinetic study of the elementary reactions of (substituted) phenol and their potential products (cyclohexanol, cyclohexanone, and cyclohexene) demonstrates that phenol selectively reacts with the in situ generated cyclohexanol or cyclohexene on Broensted acid sites. The acid-catalyzed alkylation of phenol with alcohol intermediates and alcohol dehydration are parallel reactions, which are subtly influenced by the competing hydrogenation reactions as well as by the presence of water as solvent. IR spectroscopy of adsorbed species and preliminary molecular modeling indicate that phenol and cyclohexanol enrichment in the large pores of zeolite HBEA is critical for the high activity and hydroalkylation selectivity.

  13. Modeling of Clostridium t yrobutyricum for Butyric Acid Selectivity in Continuous Fermentation

    Jianjun Du; Amy McGraw; Jamie A. Hestekin

    2014-01-01

    A mathematical model was developed to describe batch and continuous fermentation of glucose to organic acids with Clostridium tyrobutyricum . A modified Monod equation was used to describe cell growth, and a Luedeking-Piret equation was used to describe the production of butyric and acetic acids. Using the batch fermentation equations, models predicting butyric acid selectivity for continuous fermentation were also developed. The model showed that butyric acid production was a strong function...

  14. Modeling Fatty Acid Transfer from Artery to Cardiomyocyte.

    Arts, Theo; Reneman, Robert S; Bassingthwaighte, James B; van der Vusse, Ger J

    2015-12-01

    Despite the importance of oxidation of blood-borne long-chain fatty acids (Fa) in the cardiomyocytes for contractile energy of the heart, the mechanisms underlying the transfer of Fa from the coronary plasma to the cardiomyocyte is still incompletely understood. To obtain detailed insight into this transfer process, we designed a novel model of Fa transfer dynamics from coronary plasma through the endothelial cells and interstitium to the cardiomyocyte, applying standard physicochemical principles on diffusion and on the chemical equilibrium of Fa binding to carrier proteins Cp, like albumin in plasma and interstitium and Fatty Acid-Binding Proteins within endothelium and cardiomyocytes. Applying these principles, the present model strongly suggests that in the heart, binding and release of Fa to and from Cp in the aqueous border zones on both sides of the cell membranes form the major hindrance to Fa transfer. Although often considered, the membrane itself appears not to be a significant hindrance to diffusion of Fa. Proteins, residing in the cellular membrane, may facilitate transfer of Fa between Cp and membrane. The model is suited to simulate multiple tracer dilution experiments performed on isolated rabbit hearts administrating albumin and Fa as tracer substances into the coronary arterial perfusion line. Using parameter values on myocardial ultrastructure and physicochemical properties of Fa and Cp as reported in literature, simulated washout curves appear to be similar to the experimentally determined ones. We conclude therefore that the model is realistic and, hence, can be considered as a useful tool to better understand Fa transfer by evaluation of experimentally determined tracer washout curves.

  15. Modeling Fatty Acid Transfer from Artery to Cardiomyocyte.

    Theo Arts

    2015-12-01

    Full Text Available Despite the importance of oxidation of blood-borne long-chain fatty acids (Fa in the cardiomyocytes for contractile energy of the heart, the mechanisms underlying the transfer of Fa from the coronary plasma to the cardiomyocyte is still incompletely understood. To obtain detailed insight into this transfer process, we designed a novel model of Fa transfer dynamics from coronary plasma through the endothelial cells and interstitium to the cardiomyocyte, applying standard physicochemical principles on diffusion and on the chemical equilibrium of Fa binding to carrier proteins Cp, like albumin in plasma and interstitium and Fatty Acid-Binding Proteins within endothelium and cardiomyocytes. Applying these principles, the present model strongly suggests that in the heart, binding and release of Fa to and from Cp in the aqueous border zones on both sides of the cell membranes form the major hindrance to Fa transfer. Although often considered, the membrane itself appears not to be a significant hindrance to diffusion of Fa. Proteins, residing in the cellular membrane, may facilitate transfer of Fa between Cp and membrane. The model is suited to simulate multiple tracer dilution experiments performed on isolated rabbit hearts administrating albumin and Fa as tracer substances into the coronary arterial perfusion line. Using parameter values on myocardial ultrastructure and physicochemical properties of Fa and Cp as reported in literature, simulated washout curves appear to be similar to the experimentally determined ones. We conclude therefore that the model is realistic and, hence, can be considered as a useful tool to better understand Fa transfer by evaluation of experimentally determined tracer washout curves.

  16. 可替代产品库存模型的研究%Single-Period Two-Product Inventory Model with Reorder and Substitution

    李小申; 夏尊铨

    2008-01-01

    In market, many same or similar-characteristic products can substitute for each other, retailers usually adopt substitution strategy for more benefits, and excess demand for product can also be met by reorder. For single-period two-product inventory problem of this kind, we develop the profits maximization model with stochastic demands and proportional costs and revenues. We show that the objective function is concave and submodular, and therefore the optimal stock policy exists. We present the optimal conditions for stock quantities, and provide some properties of the optimal stock quantities. We explore the impacts of parameters on the profits and the optimal stock quantities. By comparison we prove that reorder, and adoption of the substitution strategy for special cases, can raise the profits and reduce the general stock level.%市场上,很多产品之间可相互替代,商家为了获得的更多的利润,经常会用一种产品替代另一种产品.不仅如此.某种产品缺货时,也可以重新进货以满足顾客的需求.我们从销售商的角度,讨论这两个因素对库存策略的影响,建立了这类问题有两个产品的单周期的利润最大化模型,证明了目标函数是凹的和子模的,从而问题的解是存在的,给出了最优订货量(原始库存)的必要条件,讨论了各参数对库存的影响.通过比较,证明了商家采取替代策略和允许再订货可以提高利润并且可减少库存总量.

  17. EFSA ; Scientific Opinion on Flavouring Group Evaluation 67, Revision 1 (FGE.67Rev.1): Consideration of 40 furan-substituted aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers evaluated by JECFA at the 65th meeting (JECFA, 2006

    Larsen, John Christian; Nørby, Karin Kristiane; Beltoft, Vibe Meister;

    evaluation is necessary, as laid down in Commission Regulation (EC) No 1565/2000. The present consideration concerns a group of 33 furan-substituted aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers evaluated by the JECFA...

  18. Amino acid substitutions in the non-structural proteins 4A or 4B modulate the induction of autophagy in West Nile virus infected cells independently of the activation of the unfolded protein response

    Ana Belen Blazquez

    2015-01-01

    Full Text Available West Nile virus (WNV is a neurotropic mosquito-borne flavivirus responsible for outbreaks of meningitis and encephalitis. Whereas the activation of autophagy in cells infected with other flaviviruses is well known, the interaction of WNV with the autophagic pathway still remains unclear and there are reports describing opposite findings obtained even analyzing the same viral strain. To clarify this controversy, we first analyzed the induction of autophagic features in cells infected with a panel of WNV strains. WNV was determined to induce autophagy in a strain dependent manner. We observed that all WNV strains or isolates analyzed, except for the WNV NY99 used, upregulated the autophagic pathway in infected cells. Interestingly, a variant derived from this WNV NY99 isolated from a persistently infected mouse increased LC3 modification and aggregation. Genome sequencing of this variant revealed only two non-synonymous nucleotide substitutions when compared to parental NY99 strain. These nucleotide substitutions introduced one amino acid replacement in NS4A and other in NS4B. Using genetically engineered viruses we showed that introduction of only one of these replacements was sufficient to upregulate the autophagic pathway. Thus, in this work we have shown that naturally occurring point mutations in the viral non structural proteins NS4A and NS4B confer WNV with the ability to induce the hallmarks of autophagy such as LC3 modification and aggregation. Even more, the differences on the induction of an autophagic response observed among WNV variants in infected cells did not correlate with alterations on the activation of the unfolded protein response (UPR, suggesting an uncoupling of UPR and autophagy during flavivirus infection. The findings here reported could help to improve the knowledge of the cellular processes involved on flavivirus-host cell interactions and contribute to the design of effective strategies to combat these pathogens.

  19. Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

    Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

    2015-10-01

    The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

  20. EFFECT OF SUBSTITUTION POSITION OF HYDROXY GROUP AT BENZOIC ACID ON THE LUMINESCENT AND DEGRADATION PROPERTIES OF POLY[DI(CARBOXYPHENYL) SUCCINATE-co-SEBACIC ANHYDRIDE]S

    Jun Fan; Hong-liang Jiang; Kang-jie Zhu

    2007-01-01

    In this work, two new diacids, di(m-carboxyphenyl) succinate (m-dCPS) and di(o-carboxyphenyl) succinate (o-dCPS), were synthesized by reaction of m-, o-hydroxy benzoic acid with succinic chloride, respectively. Their corresponding copolymers with sebacic acid (SA), P(m-dCPS:SA) and P(o-dCPS:SA), were prepared by melt copolycondensation and characterized by NMR, UV and DSC methods. Compared with inherently fluorescent poly[di(p-carboxyphenyl) succinateco-sebacic anhydride] (P(p-dCPS:SA)), P(m-dCPS:SA) and P(o-dCPS:SA) displayed different luminescent properties. P(m-dCPS:SA) could emit fluorescence under the excitation of both visible and UV light, while P(o-dCPS:SA) could only emit fluorescence when excited with UV light. Degradation rate of the two new copolyanhydrides increased with the increase of SA fraction in the copolymers. In addition, P(o-dCPS:SA) degraded more rapidly than P(m-dCPS:SA) with the same composition. Typical surface-degradation characteristics of these copolyanhydrides were observed.

  1. Crosslinked self-assemblies of lipoid acid-substituted low molecular weight (1800 Da) polyethylenimine as reductive-sensitive non-viral gene vectors

    Chen, Xiaojiao; Yuan, Zhefan; Yi, Xiaoqing; Zhuo, Renxi; Li, Feng

    2012-10-01

    In this study, amphiphilic polyethylenimine-graft-thioctic acid (PEI-TA) and polyethylenimine-graft-lauric acid (PEI-LA) were synthesized. Both PEI-TA and PEI-LA could self-assemble into micelles. Due to the existence of disulfide-linked rings at the end of hydrophobic moieties, PEI-TA could form stable micelles with disulfide crosslinked cores (PEI-TA-SS). In comparison with the PEI-LA micelle, PEI-TA-SS possessed higher DNA binding ability according to the gel retardation assay and heparin replacement assay. In vitro transfection experiments indicated that PEI-TA-SS showed comparably high transfection efficiency as compared to 25 kDa PEI. More interestingly, the luciferase expression of PEI-TA-SS was superior to that of PEI-LA at low N/P ratio, which might be ascribed to the stronger binding capacity of PEI-TA-SS facilitating the entering of PEI-TA-SS/pDNA complexes into cells.

  2. Currency Substitution and Government Revenue from Inflation Currency Substitution and Government Revenue from Inflation

    C. Luis Ramírez-Rojas

    1986-03-01

    Full Text Available Currency Substitution and Government Revenue from Inflation The purpose of this paper is to show that in the case of an open economy the calculations of revenue-maximing rates of inflation have been made using a restrictive model that assumes that domestic residents can only substitute between domestic money and goods (and real assets. The paper demonstrates that once the effects of currency substitution, so common in developing countries, are taken into account, the inflation rate that maximizes the proceeds of the inflation tax can be quite lower than would be the case when currency substitution is ignored.

  3. Diverse models for the prediction of CDK4 inhibitory activity of substituted 4-aminomethylene isoquinoline-1, 3-diones

    Monika Gupta; A K Madan

    2013-05-01

    In the present study, both classification and correlation approaches have been successfully employed for development of models for the prediction of CDK4 inhibitory activity using a dataset comprising of 52 analogues of 4-aminomethylene isoquinoline-1,3-(2,4)-dione. Decision tree, random forest, moving average analysis (MAA), multiple linear regression (MLR), partial least square regression (PLSR) and principal component regression (PCR) were used to develop models for prediction of CDK4 inhibitory activity. The statistical significance of models was assessed through specificity, sensitivity, overall accuracy, Mathew’s correlation coefficient (MCC), cross validated correlation coefficient, test, 2 for external test set (pred_r2), coefficient of correlation of predicted dataset (pred_r2Se) and intercorrelation analysis. High accuracy of prediction offers proposed models a vast potential for providing lead structures for the development of potent therapeutic agents for CDK4 inhibition.

  4. Development and Evaluation of Amino Acid Molecular Models

    Aparecido R. Silva

    2007-05-01

    Full Text Available The comprehension of structure and function of proteins has a tight relationshipwith the development of structural biology. However, biochemistry students usuallyfind difficulty to visualize the structures when they use only schematic drawings ofdidactic books. The representation of three-dimensional structures of somebiomolecules with ludic models, built with representative units, have supplied tothe students and teachers a successfully experience to better visualize andcorrelate the structures to the real molecules. The present work shows thedeveloped models and the process to produce the representative units of the mainamino acids in industrial scale. The design and applicability of the representativeunits were discussed with many teachers and some suggestions wereimplemented to the models. The preliminary evaluation and perspective ofutilization by researchers show that the work is in the right direction. At the actualstage, the models are defined, prototypes were made and will be presented in thismeeting. The moulds for the units are at the final stage of construction and trial inspecialized tool facilities. The last term will consist of an effective evaluation of thedidactic tool for the teaching/learning process in Structural Molecular Biology. Theevaluation protocol is being elaborated containing simple and objective questions,similar to those used in research on science teaching.

  5. Emergence of canine distemper virus strains with two amino acid substitutions in the haemagglutinin protein, detected from vaccinated carnivores in North-Eastern China in 2012-2013.

    Zhao, Jianjun; Zhang, Hailing; Bai, Xue; Martella, Vito; Hu, Bo; Sun, Yangang; Zhu, Chunsheng; Zhang, Lei; Liu, Hao; Xu, Shujuan; Shao, Xiqun; Wu, Wei; Yan, Xijun

    2014-04-01

    A total of 16 strains of canine distemper virus (CDV) were detected from vaccinated minks, foxes, and raccoon dogs in four provinces in North-Eastern China between the end of 2011 and 2013. Upon sequence analysis of the haemagglutinin gene and comparison with wild-type CDV from different species in the same geographical areas, two non-synonymous single nucleotide polymorphisms were identified in 10 CDV strains, which led to amino acid changes at positions 542 (isoleucine to asparagine) and 549 (tyrosine to histidine) of the haemagglutinin protein coding sequence. The change at residue 542 generated a potentially novel N-glycosylation site. Masking of antigenic epitopes by sugar moieties might represent a mechanism for evasion of virus neutralising antibodies and reduced protection by vaccination.

  6. Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers

    Kann, Nina

    2015-01-01

    © The Royal Society of Chemistry 2015. Peptidic foldamers have recently emerged as a novel class of artificial oligomers with properties and structural diversity similar to that of natural peptides, but possessing additional interesting features granting them great potential for applications in fields from nanotechnology to pharmaceuticals. Among these, foldamers containing 1,4- and 1,5-substitued triazole amino acids are easily prepared via the Cu- and Ru-catalyzed click reactions and may offer increased side chain variation, but their structural capabilities have not yet been widely explored. We here describe a systematic analysis of the conformational space of the two most important basic units, the 1,4-substitued (4Tzl) and the 1,5-substitued (5Tzl) 1,2,3-triazole amino acids, using quantum chemical calculations and NMR spectroscopy. Possible conformations of the two triazoles were scanned and their potential minima were located using several theoretical approaches (B3LYP/6-311++G(2d,2p), ωB97X-D/6-311++G(2d,2p), M06-2X/6-311++G(2d,2p) and MP2/6-311++G(2d,2p)) in different solvents. BOC-protected versions of 4Tzl and 5Tzl were also prepared via one step transformations and analyzed by 2D NOESY NMR. Theoretical results show 9 conformers for 5Tzl derivatives with relative energies lying close to each other, which may lead to a great structural diversity. NMR analysis also indicates that conformers preferring turn, helix and zig-zag secondary structures may coexist in solution. In contrast, 4Tzl has a much lower number of conformers, only 4, and these lack strong intraresidual interactions. This is again supported by NMR suggesting the presence of both extended and bent conformers. The structural information provided on these building units could be employed in future design of triazole foldamers. This journal is

  7. A quantitative structure-activity relationship study of anti-HIV activity of substituted HEPT using nonlinear models.

    Noorizadeh, Hadi; Sajjadifar, Sami; Farmany, Abbas

    2013-01-01

    We performed studies on extended series of 79 HEPT ligands (1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine), inhibitors of HIV reverse-transcriptase with anti-HIV biological activity, using quantitative structure-activity relationship (QSAR) methods that imply analysis of correlations and representation of models. A suitable set of molecular descriptors was calculated, and the genetic algorithm was employed to select those descriptors which resulted in the best-fit models. The kernel partial least square and Levenberg-Marquardt artificial neural network were utilized to construct the nonlinear QSAR models. The proposed methods will be of great significance in this research, and would be expected to apply to other similar research fields.

  8. Discovery of α-Substituted Imidazole-4-acetic Acid Analogues as a Novel Class of ρ1 γ-Aminobutyric Acid Type A Receptor Antagonists with Effect on Retinal Vascular Tone

    Krall, Jacob; Brygger, Benjamin M; Sigurðardóttir, Sara B;

    2016-01-01

    The ρ-containing γ-aminobutyric acid type A receptors (GABAA Rs) play an important role in controlling visual signaling. Therefore, ligands that selectively target these GABAA Rs are of interest. In this study, we demonstrate that the partial GABAA R agonist imidazole-4-acetic acid (IAA) is able...... to penetrate the blood-brain barrier in vivo; we prepared a series of α- and N-alkylated, as well as bicyclic analogues of IAA to explore the structure-activity relationship of this scaffold focusing on the acetic acid side chain of IAA. The compounds were prepared via IAA from l-histidine by an efficient...

  9. Modeling lanthanide series binding sites on humic acid.

    Pourret, Olivier; Martinez, Raul E

    2009-02-01

    Lanthanide (Ln) binding to humic acid (HA) has been investigated by combining ultrafiltration and ICP-MS techniques. A Langmuir-sorption-isotherm metal-complexation model was used in conjunction with a linear programming method (LPM) to fit experimental data representing various experimental conditions both in HA/Ln ratio (varying between 5 and 20) and in pH range (from 2 to 10) with an ionic strength of 10(-3) mol L(-1). The LPM approach, not requiring prior knowledge of surface complexation parameters, was used to solve the existing discrepancies in LnHA binding constants and site densities. The application of the LPM to experimental data revealed the presence of two discrete metal binding sites at low humic acid concentrations (5 mg L(-1)), with log metal complexation constants (logK(S,j)) of 2.65+/-0.05 and 7.00 (depending on Ln). The corresponding site densities were 2.71+/-0.57x10(-8) and 0.58+/-0.32x10(-8) mol of Ln(3+)/mg of HA (depending on Ln). Total site densities of 3.28+/-0.28x10(-8), 4.99+/-0.02x10(-8), and 5.01+/-0.01x10(-8) mol mg(-1) were obtained by LPM for humic acid, for humic acid concentrations of 5, 10, and 20 mg L(-1), respectively. These results confirm that lanthanide binding occurs mainly at weak sites (i.e., ca. 80%) and second at strong sites (i.e., ca. 20%). The first group of discrete metal binding sites may be attributed to carboxylic groups (known to be the main binding sites of Ln in HA), and the second metal binding group to phenolic moieties. Moreover, this study evidences heterogeneity in the distribution of the binding sites among Ln. Eventually, the LPM approach produced feasible and reasonable results, but it was less sensitive to error and did not require an a priori assumption of the number and concentration of binding sites.

  10. Matrix models with Penner interaction inspired by interacting ribonucleic acid

    Pradeep Bhadola; N Deo

    2015-02-01

    The Penner interaction known in studies of moduli space of punctured Riemann surfaces is introduced and studied in the context of random matrix model of homo RNA. An analytic derivation of the generating function is given and the corresponding partition function is derived numerically. An additional dependence of the structure combinatorics factor on (related to the size of the matrix and the interaction strength) is obtained. This factor has a strong effect on the structure combinatorics in the low regime. Databases are scanned for real ribonucleic acid (RNA) structures and pairing information for these RNA structures is computationally extracted. Then the genus is calculated for every structure and plotted as a function of length. The genus distribution function is compared with the prediction from the nonlinear (NL) model. The specific heat and distribution of structure with temperature calculated from the NL model shows that the NL inter-action is biased towards planar structures. The second derivative of specific heat changes phase from a double peaked function for small to a single peak for large . Detailed analysis reveals the presence of the double peak only for genus 0 structures, the higher genii behave normally with . Comparable behaviour is found in studies involving interactions of RNA with osmolytes and monovalent cations in unfolding experiments.

  11. Cement from magnesium substituted hydroxyapatite.

    Lilley, K J; Gbureck, U; Knowles, J C; Farrar, D F; Barralet, J E

    2005-05-01

    Brushite cement may be used as a bone graft material and is more soluble than apatite in physiological conditions. Consequently it is considerably more resorbable in vivo than apatite forming cements. Brushite cement formation has previously been reported by our group following the mixture of nanocrystalline hydroxyapatite and phosphoric acid. In this study, brushite cement was formed from the reaction of nanocrystalline magnesium-substituted hydroxyapatite with phosphoric acid in an attempt to produce a magnesium substituted brushite cement. The presence of magnesium was shown to have a strong effect on cement composition and strength. Additionally the presence of magnesium in brushite cement was found to reduce the extent of brushite hydrolysis resulting in the formation of HA. By incorporating magnesium ions in the apatite reactant structure the concentration of magnesium ions in the liquid phase of the cement was controlled by the dissolution rate of the apatite. This approach may be used to supply other ions to cement systems during setting as a means to manipulate the clinical performance and characteristics of brushite cements.

  12. Structural, magnetic and microwave absorption behavior of Co-Zr substituted strontium hexaferrites prepared using tartaric acid fuel for electromagnetic interference suppression

    Kaur, Prabhjyot; Chawla, S. K.; Narang, Sukhleen Bindra; Pubby, Kunal

    2017-01-01

    Strontium hexaferrites, doped with varying Co-Zr content (x) have been synthesized by sol-gel auto-combustion route using tartaric acid as fuel at 800 °C. X-ray diffraction and Fourier transform Infra-red have been carried out to confirm the phase formation, particle size (average 21.9-36.8 nm) and the bond formation respectively. Magnetic properties are scrutinized using vibrating sample magnetometer. Techniques like scanning electron microscopy, transmission electron microscopy and energy dispersive scattering have been employed to explore the surface morphology, particle size and composition of the nano-powders. Electromagnetic characterization of the prepared ferrites has been done using Vector Network Anlyzer in 12.4-18 GHz frequency range. The effect of calcination temperature (500-1000 °C) on the structure, morphology and magnetic properties has also been studied for x=0.2 and 800 °C has been found to be the most suitable temperature with the best magnetic properties. Increase in doping has resulted in resonance peaks in dielectric and magnetic loss spectra, leading to microwave absorption peaks. Ferrites with x=0.2, 0.8 and 1.0 have appropriate reflection loss less than -10 dB and bandwidth in Ku-band, hence can be used as effective absorbers in suppression of electromagnetic interference (EMI). The governance of impedance matching in deciding the absorption properties has been proved by using input impedance calculations.

  13. Experimental Study on Substitution of Nutrient Salt for Acetic Acid Fermentation in Frings Actator%Frings醋酸发酵营养盐替代试验研究

    张晓辉; 吴广泉; 王静; 董蓉蓉

    2014-01-01

    试验优化获得一可用于Frings醋酸发酵的自制营养盐,其物料及用量分别为:葡萄糖49.3%,酵母粉29.1%,柠檬酸铵14.6%,磷酸二氢钾3.4%,磷酸二氢钠1.7%,硫酸镁2.0%,自制营养盐与Frings营养盐按2∶8混合用于Frings醋酸发酵,可节约成本13.7%,发酵周期与Frings营养盐无明显差异。%This paper showed a homemade nutrient salt by test for acetic acid fermentation in Frings Acta-tor,this salt Includes glucose 49.3%,yeast powder 29.1%,ammonium citrate 14.6%,potassium dihydrogen phosphate 3.4%,sodium dihydrogen phosphate 1.7%,magnesium sulfate 2%.This homemade nutrient salt and the Frings nutrient salt mixed by 2∶8 can save the cost of 13.7%,and there is no significant differ-ence in the fermentation cycle.

  14. A single amino acid substitution in isozyme GST mu in Triclabendazole resistant Fasciola hepatica (Sligo strain) can substantially influence the manifestation of anthelmintic resistance.

    Fernández, V; Estein, S; Ortiz, P; Luchessi, P; Solana, V; Solana, H

    2015-12-01

    The helminth parasite Fasciola hepatica causes fascioliasis in human and domestic ruminants. Economic losses due to this infection are estimated in U$S 2000-3000 million yearly. The most common method of control is the use of anthelmintic drugs. However, there is an increased concern about the growing appearance of F. hepatica resistance to Triclabendazole (TCBZ), an anthelmintic with activity over adult and young flukes. F. hepatica has eight Glutathione S-Transferase (GST) isozymes, which are enzymes involved in the detoxification of a wide range of substrates through chemical conjugation with glutathione. In the present work we identified and characterized the GST mu gene isolated from the TCBZ-susceptible and TCBZ-resistant F. hepatica strains. Total RNA was transcribed into cDNA by reverse transcription and a 657 bp amplicon corresponding to the GST mu gene was obtained. The comparative genetic analysis of the GST mu gene of the TCBZ susceptible strain (Cullompton) and TCBZ resistant strain (Sligo) showed three nucleotide changes and one amino acid change at position 143 in the GST mu isozyme of the TCBZ-resistant strain. These results have potential relevance as they contribute better understand the mechanisms that generate resistance to anthelmintics.

  15. Sweeteners - sugar substitutes

    ... page: //medlineplus.gov/ency/article/007492.htm Sweeteners - sugar substitutes To use the sharing features on this ... that are used in place of sweeteners with sugar (sucrose) or sugar alcohols . They may also be ...

  16. An efficient synthesis of substituted benzene-1,2-dicarboxaldehydes

    ZHU Peter C; WANG Dei-Haw; LU Kaitao; MANI Neelakandha

    2007-01-01

    Substituted-benzene-1,2-dicarbaldehydes were synthesized by the reaction of substituted-1,2-bis (dibromomethyl) benzenes with fuming sulfuric acid, followed by hydrolysis, The yields were significantly improved by introducing solid sodium bicarbonate into the reaction mixture before hydrolysis and workup.

  17. An efficient synthesis of substituted benzene-1,2-dicarboxaldehydes

    ZHU; Peter; C; WANG; Der-Haw; MANI; Neelakandha

    2007-01-01

    Substituted-benzene-1,2-dicarbaldehydes were synthesized by the reaction of substituted-1,2-bis(dibromomethyl) benzenes with fuming sulfuric acid,followed by hydrolysis. The yields were signifi-cantly improved by introducing solid sodium bicarbonate into the reaction mixture before hydrolysis and workup.

  18. Control of Chemical Risks by Substitution of Harmful Substances

    Jacobsen, Thomas

    1997-01-01

    Substitution of volatile, organic solvents with non-volatile, low-toxic esters of fatty acids for cleaning purposes in offset printing has successfully been implemented in several European countries. Similar substitutions in other industrial cleaning processes seem possible, especially regarding ...

  19. The biocompatibility of a polyelectrolyte vitreous body substitute on a high resistance in vitro model of the blood-retinal barrier.

    Strotmann, Falko; Wolf, Isabel; Galla, Hans-Joachim

    2013-09-01

    The vitreous body can be regarded as a fascinating simple but important tissue, since it represents the main compartment of the eye and plays a crucial role for proper vision. Several diseases require its removal with following substitution using a liquid artificial vitreous body replacement. We explore the biocompatibility of a poly(AMPS-Na(+))-graft-poly(NIPAAm) polyelectrolyte following the innovative concept of thermo-responsive behaviour, exhibiting enhanced shear viscosity at physiological temperatures. As a powerful model for the blood-retinal barrier, we use the well-established in vitro cell culture model based on highly differentiated porcine brain capillary endothelial cells. Via the quantification of the transendothelial electrical resistance and immunocytochemical staining of tight junction proteins, we are able to show that a barrier integrity affecting impact of the polyelectrolyte was only transient and nearly reversible. Furthermore, the polyelectrolyte hydrogel is characterized by the absence of any acute cell morphology, cell vitality or proliferation affecting impacts. It does not trigger acute apoptotic processes, as can be substantiated via caspase-3 activity and DNA fragmentation assays. In view of the results of this study, it is shown that the polyelectrolyte does not affect the vitality parameters of our porcine brain capillary endothelial cells. It can be suggested that the tested thermo-responsive polyelectrolyte does not affect the sensitive retinal barrier integrity. Thus from the cellular tolerance it might serve as a potential liquid artificial vitreous body replacement to overcome the most prominent difficulties of common vitreal endotamponades.

  20. La política fiscal en el modelo de sustitución de importaciones Fiscal policy in the import substitution model

    Giraldo Giraldo César

    1996-12-01

    Full Text Available El modelo de sustitución de importaciones, el manejo de las finanzas públicas, que buscaba redistribuir el ingreso y fomentar la producción nacional, contribuyó al proceso de industrialización y modernización de América Latina. Las funciones fiscales se alejaron de su orientación inicial porque cambiaron las condiciones económicas que dieron origen al modelo, y porque los controles impuestos para racionalizar el manejo de las divisas y fomentar la producción se convirtieron en privilegios que promovían una economía rentista que desestimuló una inversión productiva, generó una alta concentración del ingreso y limitó la expansión del mercado interno.In the import substitution model the management of public finance, which attempts to redistribute in comeand promote national production, contributed to the process of industrialization and modernization in latin America. The fiscal functions moved away from their initial orientation because the economic conditions from which the model originated had changed and because the controls put in force to rationalize the handling of foreign currency and promote productionturned into privileges which promoted a rentier economy, which discouraged productive investment, generated a high concentration of income, and limited the expansion of the internal market.

  1. Substitution between cars within the household

    De Borger, Bruno; Mulalic, Ismir; Rouwendal, Jan

    2016-01-01

    .98 and 1.41 for the primary and secondary cars, respectively. Accounting for substitution effects, these figures reduce to, respectively, 0.32 and 0.45. Consistent with substitution behaviour, we find that the fuel price elasticity of fuel demand exceeds the elasticity of kilometre demands with respect...... to the fuel price; the difference strongly increases at the highest deciles of the distribution of kilometre demand. Extending the model to account for driver heterogeneity and the role of car characteristics confirmed the relevance of substitution between cars within the household. We found strong evidence......’ fuel efficiency choices are related to their price sensitivity....

  2. Synthesis of substituted pyrazines

    Pagoria, Philip F.; Zhang, Mao Xi

    2016-10-04

    A method for synthesizing a pyrazine-containing material according to one embodiment includes contacting an iminodiacetonitrile derivative with a base and a reagent selected from a group consisting of hydroxylamine, a hydroxylamine salt, an aliphatic primary amine, a secondary amine, an aryl-substituted alkylamine a heteroaryl-substituted alkyl amine, an alcohol, an alkanolamine and an aryl alcoholamine. Additional methods and several reaction products are presented. ##STR00001##

  3. Modeling of Clostridium tyrobutyricum for Butyric Acid Selectivity in Continuous Fermentation

    Jianjun Du

    2014-04-01

    Full Text Available A mathematical model was developed to describe batch and continuous fermentation of glucose to organic acids with Clostridium tyrobutyricum. A modified Monod equation was used to describe cell growth, and a Luedeking-Piret equation was used to describe the production of butyric and acetic acids. Using the batch fermentation equations, models predicting butyric acid selectivity for continuous fermentation were also developed. The model showed that butyric acid production was a strong function of cell mass, while acetic acid production was a function of cell growth rate. Further, it was found that at high acetic acid concentrations, acetic acid was metabolized to butyric acid and that this conversion could be modeled. In batch fermentation, high butyric acid selectivity occurred at high initial cell or glucose concentrations. In continuous fermentation, decreased dilution rate improved selectivity; at a dilution rate of 0.028 h−1, the selectivity reached 95.8%. The model and experimental data showed that at total cell recycle, the butyric acid selectivity could reach 97.3%. This model could be used to optimize butyric acid production using C. tyrobutyricum in a continuous fermentation scheme. This is the first study that mathematically describes batch, steady state, and dynamic behavior of C. tyrobutyricum for butyric acid production.

  4. Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) Impairs Viral Release and Hampers BST-2 Antagonism

    Dufrasne, François E.; Lombard, Catherine; Goubau, Patrick; Ruelle, Jean

    2016-01-01

    BST-2 or tetherin is a host cell restriction factor that prevents the budding of enveloped viruses at the cell surface, thus impairing the viral spread. Several countermeasures to evade this antiviral factor have been positively selected in retroviruses: the human immunodeficiency virus type 2 (HIV-2) relies on the envelope glycoprotein (Env) to overcome BST-2 restriction. The Env gp36 ectodomain seems involved in this anti-tetherin activity, however residues and regions interacting with BST-2 are not clearly defined. Among 32 HIV-2 ROD Env mutants tested, we demonstrated that the asparagine residue at position 659 located in the gp36 ectodomain is mandatory to exert the anti-tetherin function. Viral release assays in cell lines expressing BST-2 showed a loss of viral release ability for the HIV-2 N659D mutant virus compared to the HIV-2 wild type virus. In bst-2 inactivated H9 cells, those differences were lost. Subtilisin treatment of infected cells demonstrated that the N659D mutant was more tethered at the cell surface. Förster resonance energy transfer (FRET) experiments confirmed a direct molecular link between Env and BST-2 and highlighted an inability of the mutant to bind BST-2. We also tested a virus presenting a truncation of 109 amino acids at the C-terminal part of Env, a cytoplasmic tail partial deletion that is spontaneously selected in vitro. Interestingly, viral release assays and FRET experiments indicated that a full Env cytoplasmic tail was essential in BST-2 antagonism. In HIV-2 infected cells, an efficient Env-mediated antagonism of BST-2 is operated through an intermolecular link involving the asparagine 659 residue as well as the C-terminal part of the cytoplasmic tail. PMID:27754450

  5. Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env Impairs Viral Release and Hampers BST-2 Antagonism

    François E. Dufrasne

    2016-10-01

    Full Text Available BST-2 or tetherin is a host cell restriction factor that prevents the budding of enveloped viruses at the cell surface, thus impairing the viral spread. Several countermeasures to evade this antiviral factor have been positively selected in retroviruses: the human immunodeficiency virus type 2 (HIV-2 relies on the envelope glycoprotein (Env to overcome BST-2 restriction. The Env gp36 ectodomain seems involved in this anti-tetherin activity, however residues and regions interacting with BST-2 are not clearly defined. Among 32 HIV-2 ROD Env mutants tested, we demonstrated that the asparagine residue at position 659 located in the gp36 ectodomain is mandatory to exert the anti-tetherin function. Viral release assays in cell lines expressing BST-2 showed a loss of viral release ability for the HIV-2 N659D mutant virus compared to the HIV-2 wild type virus. In bst-2 inactivated H9 cells, those differences were lost. Subtilisin treatment of infected cells demonstrated that the N659D mutant was more tethered at the cell surface. Förster resonance energy transfer (FRET experiments confirmed a direct molecular link between Env and BST-2 and highlighted an inability of the mutant to bind BST-2. We also tested a virus presenting a truncation of 109 amino acids at the C-terminal part of Env, a cytoplasmic tail partial deletion that is spontaneously selected in vitro. Interestingly, viral release assays and FRET experiments indicated that a full Env cytoplasmic tail was essential in BST-2 antagonism. In HIV-2 infected cells, an efficient Env-mediated antagonism of BST-2 is operated through an intermolecular link involving the asparagine 659 residue as well as the C-terminal part of the cytoplasmic tail.

  6. In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions.

    Gangopadhyay, Jaya Pal; Jiang, Shu-qin; van Berkel, Patrick; Paulus, Henry

    2003-01-20

    Protein splicing is a self-catalyzed process involving the excision of an intervening polypeptide sequence, the intein, and joining of the flanking polypeptide sequences, the extein, by a peptide bond. We have studied the in vitro splicing of erythropoietin (EPO) using a truncated form of the Mycobacterium tuberculosis RecA mini-intein in which the homing endonuclease domain was replaced with a hexahistidine sequence (His-tag). The intein was inserted adjacent to cysteine residues to assure that the spliced product had the natural amino acid sequence. When expressed in Escherichia coli, intein-containing EPO was found entirely as inclusion bodies but could be refolded in soluble form in the presence of 0.5 M arginine. Protein splicing of the refolded protein could be induced with a reducing agent such as DTT or tris(2-carboxyethyl)phosphine and led to the formation of EPO and mini-intein along with some cleavage products. Protein splicing mediated by the RecA intein requires the presence of a cysteine residue adjacent to the intein insertion site. We compared the efficiencies of protein splicing adjacent to three of the four cysteine residues of EPO (Cys29, Cys33 and Cys161) and found that insertion of intein adjacent to Cys29 allowed far more efficient protein splicing than insertion adjacent to Cys33 or Cys161. For ease of purification, our experiments involved a His-tagged EPO fusion protein and a His-tagged intein and the spliced products (25 kDa EPO and 24 kDa mini-intein) were identified by Western blotting using anti-EPO and anti-His-tag antibodies and by mass spectroscopy. The optimal splicing yield at Cys29 (40%) occurred at pH 7.0 after refolding at 4 degrees C and splicing for 18 h at 25 degrees C in the presence of 1 mM DTT.

  7. Adsorption of 2-naphthalenesulfonic acid/sulfuric acid/sulfurous acid from aqueous solution by iron-impregnated weakly basic resin:Equilibrium and model

    Changhai Li; Dongmei Jia

    2016-01-01

    Commercial grade weakly basic resin D301 was impregnated with iron through a simple method using ferric chloride. Experiments for single, bisolute and trinary competitive adsorption were carried out to investigate the adsorption behavior of 2-naphthalenesulfonic acid (NSA), sulfuric acid and sulfurous acid from their solution at 298K onto the novel hybrid iron impregnated D301(Fe-D301). Adsorption affinity of NSA on Fe-D301 was found to be much higher than that of sulfuric acid, while adsorption affinity of sulfuric acid was slightly higher than that of sulfurous acid. The data of single-solute adsorption were fitted to the Langmuir model and the Freundlich adsorption model. The non-ideal competitive adsorbed model coupled with the single-solute adsorp-tion models were used to predict the bisolute and trinary-solute competitive adsorption equilibria. The NICM coupled with the Langmuir model yields the favorable representation of the bisolute and trinary-solute compet-itive adsorption behavior.

  8. Length and amino acid sequence of peptides substituted for the 5-HT3A receptor M3M4 loop may affect channel expression and desensitization.

    Nicole K McKinnon

    Full Text Available 5-HT3A receptors are pentameric neurotransmitter-gated ion channels in the Cys-loop receptor family. Each subunit contains an extracellular domain, four transmembrane segments (M1, M2, M3, M4 and a 115 residue intracellular loop between M3 and M4. In contrast, the M3M4 loop in prokaryotic homologues is <15 residues. To investigate the limits of M3M4 loop length and composition on channel function we replaced the 5-HT3A M3M4 loop with two to seven alanine residues (5-HT3A-A(n = 2-7. Mutants were expressed in Xenopus laevis oocytes and characterized using two electrode voltage clamp recording. All mutants were functional. The 5-HT EC(50's were at most 5-fold greater than wild-type (WT. The desensitization rate differed significantly among the mutants. Desensitization rates for 5-HT3A-A(2, 5-HT3A-A(4, 5-HT3A-A(6, and 5-HT3A-A(7 were similar to WT. In contrast, 5-HT3A-A(3 and 5-HT3A-A(5 had desensitization rates at least an order of magnitude faster than WT. The one Ala loop construct, 5-HT3A-A(1, entered a non-functional state from which it did not recover after the first 5-HT application. These results suggest that the large M3M4 loop of eukaryotic Cys-loop channels is not required for receptor assembly or function. However, loop length and amino acid composition can effect channel expression and desensitization. We infer that the cytoplasmic ends of the M3 and M4 segments may undergo conformational changes during channel gating and desensitization and/or the loop may influence the position and mobility of these segments as they undergo gating-induced conformational changes. Altering structure or conformational mobility of the cytoplasmic ends of M3 and M4 may be the basis by which phosphorylation or protein binding to the cytoplasmic loop alters channel function.

  9. Modelling the cloud condensation nucleus activity of organic acids

    Z. Varga

    2007-04-01

    Full Text Available In this study vapour pressure osmometry was used to determine water activity in solutions of organic acids. The surface tension of the solutions was also monitored in parallel and then Köhler curves were calculated for nine organic acids (oxalic, malonic, succinic, glutaric, adipic acid, maleic acid, malic acid, citric acid and pinonic acid. Surface tension depression is negligible for most of the organic acids in dilute (≤1 w/w% solutions. Therefore, these compounds affect the supersaturation only in the beginning phase of droplet formation but not necessarily at the critical size. An exception is cis-pinonic acid which remarkably depress surface tension also in dilute (0.1 w/w% solution and hence at the critical point. The surface tension of organic acid solutions is influenced by the solubility of the compound, the length of the carbon chain and also by the polar functional groups present in the molecule. Similarly to surface tension solubility plays an important role also in water activity: compounds with higher solubility (e.g. malonic, maleic, and glutaric acid reduce water activity significantly in the early phase of droplet formation while less soluble acids (e.g. succinic and adipic acid are saturated in small droplets and the solution starts diluting only in bigger droplets. As a consequence, compounds with lower solubility have a minor effect on water activity in the early phase of droplet formation. To deduce the total effect Köhler curves were calculated and critical supersaturations were determined for the organic acids using measured surface tension and water activity. It was found that critical supersaturation grew with growing carbon number. Oxalic acid had the lowest critical supersaturation in the size range studied and it was comparable to the activation of ammonium sulfate. The Sc values obtained in this study were compared to data from CCNC measurements. In most cases good agreement was found.

  10. Mechanistic Study of the Acid Degradation of Lignin Model Compounds

    Sturgeon, M.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.

    2012-01-01

    Lignin is a major constituent of biomass, which remains underutilized in selective biomass conversion strategies to renewable fuels and chemicals. Here we are interested in understanding the mechanisms related to the acid deconstruction of lignin with a combined theoretical and experimental approach. Two model dimers with a b-O-4 aryl ether linkage (2-phenoxy-1-phenethanol and 2-phenoxy-1-phenyl-1,3 propanediol) and model dimmers with an a-O-4 aryl ether linkage were synthesized and deconstructed in H2SO4. The major products of the acidolysis of the b-O-4 compounds consisted of phenol and two aldehydes, phenylacetaldehyde and benzaldehyde. Quantum mechanical calculations were employed to elucidate possible deconstruction mechanisms with transition state theory. To confirm proposed mechanisms several possible intermediates were studied under similar acidolysis conditions. Although the resonance time for cleavage was on the order several hours, we have shown that the cleavage of the aryl ether linkage affords phenol and aldehydes. We would next like to utilize our mechanism of aryl ether cleavage in actual lignin.

  11. Evaluation of polylactic acid nanoparticles safety using Drosophila model.

    Legaz, Sophie; Exposito, Jean-Yves; Lethias, Claire; Viginier, Barbara; Terzian, Christophe; Verrier, Bernard

    2016-10-01

    Cytotoxicity of nanoparticles and their sub-lethal effect on cell behavior and cell fate are a high topic of studies in the nanomaterial field. With an explosion of nanoparticle types (size, shape, polarity, stiffness, composition, etc.), Drosophila has become an attractive animal model for high throughput analysis of these nanocarriers in the drug delivery field with applications in cancer therapy, or simply to generate a fast and complete cytotoxic study of a peculiar nanoparticle. In respect to that, we have conducted an in cellulo study of poly(lactic acid) (PLA) nanoparticle cytotoxicity, and determined that near lethal nanoparticle doses, oxidative stress as well as P53 and ATP pathways may lead to cell cycle arrest at G1, and ultimately to cell death. Neither viability nor the development of Drosophila larvae are affected by the ingestion of PLA nanoparticles at sub-lethal concentrations. Drosophila will be a useful model to study PLA and PLA-modified nanoparticle toxicity, and nanoparticle fate after ingestion.

  12. Amino acid substitution in P3 of Soybean mosaic virus to convert avirulence to virulence on Rsv4-genotype soybean is influenced by the genetic composition of P3.

    Wang, Y; Khatabi, B; Hajimorad, M R

    2015-04-01

    The modification of avirulence factors of plant viruses by one or more amino acid substitutions converts avirulence to virulence on hosts containing resistance genes. Limited experimental studies have been conducted on avirulence/virulence factors of plant viruses, in particular those of potyviruses, to determine whether avirulence/virulence sites are conserved among strains. In this study, the Soybean mosaic virus (SMV)-Rsv4 pathosystem was exploited to determine whether: (i) avirulence/virulence determinants of SMV reside exclusively on P3 regardless of virus strain; and (ii) the sites residing on P3 and crucial for avirulence/virulence of isolates belonging to strain G2 are also involved in virulence of avirulent isolates belonging to strain G7. The results confirm that avirulence/virulence determinants of SMV on Rsv4-genotype soybean reside exclusively on P3. Furthermore, the data show that sites involved in the virulence of SMV on Rsv4-genotype soybean vary among strains, with the genetic composition of P3 playing a crucial role.

  13. SINTESIS PATI SAGU IKATAN SILANG FOSFAT BERDERAJAT SUBSTITUSI FOSFAT TINGGI DALAM SUASANA ASAM [Synthesis of Cross-Linked Sago Starch Phosphate with the Highest Degree of Substitution of Phosphate Under Acidic Condition

    Jorion Romengga*

    2011-12-01

    Full Text Available Cross-linked sago starch phosphate (SgP with high phosphorus contents was successfully synthesized by reacting sago with a mixture of primary and secondary sodium phosphates under acidic condition. The experimental variables investigated include pH, temperature, reaction time, and mixture rate. The physicochemical properties evaluated were moisture, swelling power, water binding capacity, transmittance (%T and percent amylose (%Am, while the pasting properties examined were pasting time, pasting temperature, viscosity at peak, final, and setback. The granule structure was observed by scanning electron microscope and X-ray diffraction. The results showed that the maximum degree of phosphate substitution was obtained at pH of 6.50, 40°C, 20 minutes of reaction time and 300 rpm of mixing rate. The physicochemical (%T and %Am and pasting (viscosity at peak, final, and setback properties of SgP were significantly different (P<0.01 from Sg. Structure of SgP was characterized by FT-IR and the results indicated a new absorption peak at 2362.87 cm-1 which was characterized as the phospho-diester (RO-PO3-R’ stretching vibration. In the fingerprint area, there were two new absorption peaks at 1242.05 and 989.79 cm-1 which were characterized as the P=O and C-O-P vibration, respectively. Sago granules were substantially altered after cross-linking.

  14. Neuraminidase Receptor Binding Variants of Human Influenza A(H3N2) Viruses Resulting from Substitution of Aspartic Acid 151 in the Catalytic Site: a Role in Virus Attachment?▿

    Lin, Yi Pu; Gregory, Victoria; Collins, Patrick; Kloess, Johannes; Wharton, Stephen; Cattle, Nicholas; Lackenby, Angie; Daniels, Rodney; Hay, Alan

    2010-01-01

    Changes in the receptor binding characteristics of human H3N2 viruses have been evident from changes in the agglutination of different red blood cells (RBCs) and the reduced growth capacity of recently isolated viruses, particularly in embryonated eggs. An additional peculiarity of viruses circulating in 2005 to 2009 has been the poor inhibition of hemagglutination by postinfection ferret antisera for many viruses isolated in MDCK cells, including homologous reference viruses. This was shown not to be due to an antigenic change in hemagglutinin (HA) but was shown to be the result of a mutation in aspartic acid 151 of neuraminidase (NA) to glycine, asparagine, or alanine, which caused an oseltamivir-sensitive agglutination of RBCs. The D151G substitution was shown to cause a change in the specificity of NA such that it acquired the capacity to bind receptors, which were refractory to enzymatic cleavage, without altering its ability to remove receptors for HA. Thus, the inhibition of NA-dependent agglutination by the inclusion of oseltamivir carboxylate in the assay was effective in restoring the anti-HA specificity of the hemagglutination inhibition (HI) assay for monitoring antigenic changes in HA. Since the NA-dependent binding activity did not affect virus neutralization, and virus populations in clinical specimens possessed, at most, low levels of the “151 mutant,” the biological significance of this feature of NA in, for example, immune evasion is unclear. It is apparent, however, that an important role of aspartic acid 151 in the activity of NA may be to restrict the specificity of the NA interaction and its receptor-destroying activity to complement that of HA receptor binding. PMID:20410266

  15. Solvent effect on the stability and properties of platinum-substituted borirene and boryl isomers: The polarizable continuum model

    Ghiasi, Reza; Peikari, Ali

    2016-11-01

    The structure and properties of platinum borirene complex trans-[Cl(PMe3)2Pt{μ-BN(SiMe3)2C=C}Ph] and its isomer the platinum boryl complex trans-[Cl(PMe3)2PtBN(SiMe3)2C≡CPh] were investigated theoretically. The solvent effect on the stability, structural parameters, frontier orbital energies, HOMO-LUMO gaps, and hardness of isomers was investigated using the polarizable continuum model (PCM). It was found that borirene isomer is the most stable isomer in the gas phase and solvent. The calculated results show that the presence of solvent reduces the frontier orbital energy of the studied molecules. Geometries obtained from calculations were used to perform NBO analysis.

  16. Quantum chemistry based quantitative structure-activity relationships for modeling the (sub)acute toxicity of substituted mononitrobenzenes in aquatic systems

    Zvinavashe, E.; Murk, A.J.; Vervoort, J.; Soffers, A.E.M.F.; Freidig, A.; Rietjens, I.M.C.M.

    2006-01-01

    Fifteen experimental literature data sets on the acute toxicity of substituted nitrobenzenes to algae (Scenedesmus obliquus, Chlorella pyrenoidosa, C. vulgaris), daphnids (Daphnia magna, D. carinata), fish (Cyprinus carpio, Poecilia reticulata), protozoa (Tetrahymena pyriformis), bacteria (Phosphoba

  17. Mechanisms of network collapse in GeO2 glass: high-pressure neutron diffraction with isotope substitution as arbitrator of competing models

    Wezka, Kamil; Salmon, Philip S.; Zeidler, Anita; Whittaker, Dean A. J.; Drewitt, James W. E.; Klotz, Stefan; Fischer, Henry E.; Marrocchelli, Dario

    2012-12-01

    The structure of the network forming glass GeO2 is investigated by making the first application of the method of in situ neutron diffraction with isotope substitution at pressures increasing from ambient to 8 GPa. Of the various models, the experimental results are in quantitative agreement only with molecular dynamics simulations made using interaction potentials that include dipole-polarization effects. When the reduced density ρ/ρ0 ≳ 1.16, where ρ0 is the value at ambient pressure, network collapse proceeds via an interplay between the predominance of distorted square pyramidal GeO5 units versus octahedral GeO6 units as they replace tetrahedral GeO4 units. This replacement necessitates the formation of threefold coordinated oxygen atoms and leads to an increase with density in the number of small rings, where a preference is shown for sixfold rings when ρ/ρ0 = 1 and fourfold rings when ρ/ρ0 = 1.64.

  18. Bone Regeneration Using a Mixture of Silicon-Substituted Coral HA and β-TCP in a Rat Calvarial Bone Defect Model

    Jiyeon Roh

    2016-02-01

    Full Text Available The demand of bone graft materials has been increasing. Among various origins of bone graft materials, natural coral composed of up to 99% calcium carbonate was chosen and converted into hydroxyapatite (HA; silicon was then substituted into the HA. Then, the Si-HA was mixed with β-tricalcium phosphate (TCP in the ratios 100:0 (S100T0, 70:30 (S70T30, 60:40 (S60T40, and 50:50 (S50T50. The materials were implanted for four and eight weeks in a rat calvarial bone defect model (8 mm. The MBCPTM (HA:β-TCP = 60:40, Biomatalante, Vigneux de Bretagne, France was used as a control. After euthanasia, the bone tissue was analyzed by making histological slides. From the results, S60T40 showed the fastest bone regeneration in four weeks (p < 0.05. In addition, S60T40, S50T50, and MBCPTM showed significant new bone formation in eight weeks (p < 0.05. In conclusion, Si-HA/TCP showed potential as a bone graft material.

  19. 3-Substituted-4-hydroxycoumarin as a new scaffold with potent CDK inhibition and promising anticancer effect: Synthesis, molecular modeling and QSAR studies.

    Abdel Latif, Nehad A; Batran, Rasha Z; Khedr, Mohammed A; Abdalla, Mohamed M

    2016-08-01

    A new series of 3-substituted-4-hydroxycoumarin derivatives was designed, synthesized, and evaluated for CDK inhibiting and anticancer activities. All the synthesized target compounds showed remarkably high affinity and selectivity towards CDK1B, compared to flavopiridol, with Ki values in the low nanomolar range (Ki=0.35-0.88nM). Most of them elicited considerable inhibiting effect against CDK9T1 (Ki=3.26-23.45nM). Moreover, all the target compounds were tested in vitro against eighteen types of human tumor cell lines. The hydrazone 3a, N-phenylpyrazoline derivative 6b and 2-aminopyridyl-3-carbonitrile derivative 8c were the most potent anticancer agents against MCF-7 breast cancer cell line (IC50=0.21, 0.21 and 0.23nM, respectively). The target compounds 3a, 6b and 8c were further evaluated in MCF-7 breast cancer mouse xenograft model and showed in vivo efficacy at 10mg/kg dose. The docking study confirmed a unique binding mode in the active site of CDK1B with better score than flavopiridol. Quantitative structure activity relationship study was done and revealed a highly predictive power R(2) of 0.81.

  20. ESR, electrochemical, molecular modeling and biological evaluation of 4-substituted and 1,4-disubstituted 7-nitroquinoxalin-2-ones as potential anti- Trypanosoma cruzi agents

    Aguilera-Venegas, Benjamín; Olea-Azar, Claudio; Norambuena, Ester; Arán, Vicente J.; Mendizábal, Fernando; Lapier, Michel; Maya, Juan Diego; Kemmerling, Ulrike; López-Muñoz, Rodrigo

    2011-03-01

    Electrochemical and ESR studies were carried out in this work with the aim of characterizing the reduction mechanisms of 4-substituted and 1,4-disubstituted 7-nitroquinoxalin-2-ones by means of cyclic voltammetry in DMSO as aprotic solvent. Two reduction mechanisms were found for these compounds: the first, for compounds bearing a labile hydrogen by following a self-protonation mechanism (ECE steps), and the second, for compounds without labile hydrogen, based on a purely electrochemical reduction mechanism (typical of nitroheterocycles). The electrochemical results were corroborated using ESR spectroscopy allowing us to propose the hyperfine splitting pattern of the nitro-radical, which was later corroborated by the ESR simulation spectra. All these compounds were assayed as growth inhibitors against Trypanosoma cruzi: first, on the non-proliferative (and infective) form of the parasite (trypomastigote stage), and then, the ones that displayed activity, were assayed on the non-infective form (epimastigote stage). Thus, we found four new compounds highly active against T. cruzi. Finally, molecular modeling studies suggest the inhibition of the trypanothione reductase like one of the possible mechanisms involved in the trypanocidal action.